CMB Education » Study Programme in Biomedicine » DiscussionsAndSelfStudy

Cell biology and Genetics - course module Cell biology 1

Introduction to discussion and self-studies in Cell biology

  • Discussions are a very good support of active learning. Ideally, all the members in a group come prepared to the discussion and actively contribute to the discussion. On this course, there are discussions both with and without teacher support. Note that there are no discussions that are to be led by a teacher. Moreover, none of the discussions are obligatory – but the concepts, functions and mechanisms discussed are the same or similar as the questions in the final exam.
  • On this course, we use the word ”seminar” as defined in the traditional academic sense. This means that the seminar participants take turns prepare a short or a long presentation (with or without an ”opponent”), present it to the rest of the seminar members in a seminar session. The seminar topic is then discussed, and the discussion can be facilitated by a seminar leader.
  • You may have participated in activities termed ”seminars” which basically are situations where the participants discuss pre-prepared questions. In general, it would be more correct to call such learning situations discussions. They would definitely not be called seminars in departments doing scientifíc research in cell biology.
  • Think about the basic questions in all learning. Most often they are one of the following types:
    • What?
    • How?
    • Why?
    • How does one know it?
  • Which do you think is the most important question?
  • These questions have been written in English but of course you are free to discuss them in any language that you wish. Conceptual thinking is often enhanced when one deals with questions using two languages and study results in general are better or equally good as when compared to single-language teaching.

Self-study module 1

Study the way Alberts is constructed; take a look at the beginning of the book where the special features in the book are listed (p ix), likewise the topics covered in the book (p xi-xxvii). There is a very good glossary and a complete index in the end. Finally read pages the first chapter from Alberts. Don’t forget to use the reading specifications (läsanvisningarna) for important concepts.

Self-study module 2

Spend the afternoon reviewing the contents covered so far: the DNA lectures, microscopy and the first laboratory practical. Go through your lecture notes, any powerpoints used and the pages and chapters indicated in the Alberts.

Read the complete compendium to the first laboratory practical and go through your notes from the introductory lecture. Pay special attention to the safety instructions. Do not forget to study the specifications for the plasmids used. Note down any questions that you may have. Try to simulate in your mind all the steps in the experiments you will be conducting. Plan also how you will make notes.

Discussion 1

The students are allocated to different group rooms in their standard course groups. The students discuss through the questions in this compendium using the cell biology textbook, notes from lectures, or whatever resources are found useful or are available. Work on the questions starts when the students are in place. They should not wait for a start signal from a teacher. One teacher helps two rooms with students.

A teacher will be there to give support and to help the students but not to lead the discussion. The students decide on their own when they have finished working on a particular question. This is extremely good practise for the future career in biomedicine. This discussion as all discussions on this course is also an exercise in teamwork and leadership and the success of the discussion mostly depends on the active participation of the students in the group. An ideal discussion would also spawn further questions. The teachers can also actively participate in the discussion and present further topics of interest.

General cell biology questions:

1. We often state (jokingly) that ”the cell is the most important organ in the body”. Why is the cell so central in biomedical and medical research?

2. Make a list of the ten most central functions of the human body (such as hearing, sight etc) and a corresponding list of the functions in the human cell (or different types of cells). Can you see connections between the cellular functions and the functions on the whole organism?

3. Why are different animal models used in cell biological research?

4. Why can the results from animal models be related to medical research?

5. How similar are we to other organisms? How do we know that?

6. Imagine that a new species of life is found on the planet Mars – how would you go about finding out if the life there is related to the life on Earth?

Microscopy questions:

1. What kind of microscopes (include staining method if applicable) would you use to study the following:

  • Live yeast cells
  • HIV-particles
  • Mitotic chromosomes
  • Bacteria from an infected wound
  • Intracellular structures such as ribosomes
2. What limits the resolution of light microscopes?

3. Why is it that samples often have to be ”fixed” before they can be studied?

4. Why is it that samples often have to be stained before they can be studied?

5. What is meant by ”image processing” in microscopy?

6. What is a microtome? How are they used in cell biology?

7. What is meant by ”fluorescence”?

8. Draw a schematic picture of how antibodies can be used to specifically detect molecules in the cell.

9. What is the primary advantage of a confocal fluorescence microscope compared to a conventional microscope?

10. How small things can one see with an electron microscope?

11. What is meant by immunogold electron microscopy?

12. What kind of samples are studied using scanning electron microscopy?

13. What kind of samples are studied using EM tomography?

Self-study module 3

Finish reviewing the material from the DNA lectures from the previous week.

Self-study module 4

Scan the Alberts materials for prokaryotic cell biology (see study specifications to Alberts) using your notes from the lectures as support. Note any questions that you may have and save the questions to Discussion 2. It is very good idea to make notes while you read – for example to note down the function of all the different important concepts that the study specifications take up. Some may even like to draw their own schematic pictures of any structures and functions – this is called concept mapping.

Try to figure the answers to the following questions on your own – you may even find the answer in Alberts.

1. Why are most bacterial cells so small? Why are there very few bacteria the size of e g yeast cells or even bigger?

2. In higher eukaryotic organisms, cells differentiate to form different tissues (vävnader) and organs. Are bacterial biofilms a kind of a prokaryotic tissue? Motivate your answer.

3. How do bacterial cells communicate with each other?

4. Do bacterial cells communicate (send or receive signals) with eukaryotic cells? Can you give any examples?

5. Do bacteria have mitosis? Motivate your answer.

6. What would be an opportunistic pathogen?

7. How do bacteria move? What directs their movement?

Discussion 2 with teacher support: first day

  • Bring the compendium for the first practical plus your Alberts to the discussions on both afternoons.

Questions from the first practical

1. Why is it important to contain (avoid spreading) genetically modified organisms?

2. Why is E. coli used as a model organism in cell biology?

3. How did you genetically modify the bacteria in the exercise?

4. Why was ampicillin used? How does it work?

5. Did all your transformations work? Did something grow on the plates?

6. Was the thing growing on the plates bacteria? How do you know that?

7. Did all plasmids produce fluorescence? Why or why not?

8. Look at the specifications of the plasmid pEF/myc/mito/gfp in the end of the compendium with the DNA sequence. Identify the following features:

  • The promoter region with the TATA box – locate them in the DNA sequence. What is their function? Did this promoter work in E. coli? Why or why not?
  • Locate the start of transcription and the start of translation in the DNA sequence.
  • The intron – where is it located in this gene in reference to the coding sequence?
  • How can the plasmid be replicated and maintained in the bacterial cell? What is the plasmid part responsible for this function called?

Questions on DNA replication

1. All cells must replicate their DNA before each cell division. Why is it that DNA has to be replicated extremely accurately, with very few errors?

2. Why are specific RNA-primers needed? How are they created, used and deleted?

3. How is DNA replicated in the end of linear chromosomes? What are the structures at the ends of chromosomes called? What is their cellular function?

4. What are so called mobile elements in genomes? Where do they come from? What is their biological function?

Questions on DNA-repair

1. How often do mutations occur? What is optimal for organisms, low or high mutation rates? Is the ideal situation without any mutations at all?

2. How do cells know that there is something wrong with the DNA?

3. After DNA replication, how could cells differentiate between the ”old” and the ”new ” strand in case there is a mismatch as a result of bad replication?

4. What are the principle ways of DNA repair?

Questions on transcription

1. What is the function of the promoter and the terminator?

2. What kind of RNA polymerases does the cell utilize? Why are there different RNA polymerases?

3. What kind of different RNA molecules are there in the cell?

4. Why is it called “transcription”?

5. Why does transcription initiation in eukaryotes require so many different proteins?

Questions on RNA processing

1. What are the different steps in RNA processing in eukaryotes?

2. What is their significance or biological function?

3. What is alternative splicing? What is its biological significance?

4. How is the mRNA transported from the nucleus?

Questions on translation

1. Why is it called “translation”?

2. What is a reading frame? How many are there (potentially) in a double-stranded DNA molecule?

3. Where does translation occur?

4. What is a polysome?

5. What is meant by the genetic code being “redundant”? Give an example.

Questions on gene regulation

1. Why is it that gene activity must be regulated?

2. Make a list of the different steps where gene activity can be regulated and give a specific example of how it could be done.

3. Make a list of different types of DNA sequences and proteins involved in the regulation of transcriptional activity complete with a list of their functions. Why are there so many different types of sequences or proteins?

4. Give examples of how one could measure the activity of a single gene in a cell or in an organism.

Discussion 2 with teacher support: second day


The second part of the Discussion 2 deals with the comparative perspective between prokaryotic and eukaryotic cells. Again, bring your Alberts and the compendium to the first practical.

Questions on genetics:

1. How is the bacterial chromosome different from eukaryotic chromosomes? Are there any differences in the organisation of genes?

2. What is a plasmid? Where are they found? What is their function in nature? How can they be used in cell biological research?

3. What are bacteriophages? How can they be used in cell biological research?

4. What is meant by an operon? Do eukaryotes have them? What are the advantages of operons?

5. What is the function of a Shine Dalgarno sequence? Why do bacteria require them?

6. Identify the following elements in the DNA sequences of the promoters in the plasmids that gave fluorescence during the first practical.

  • The lac promoter
  • CAP binding region (function?)
  • -35 region (function?)
  • transcription start point
  • lac operator (function)
  • ribosome binding site (function)
  • start codon for translation
  • any introns?
7. What are the principal differences in the pathway from DNA to protein between prokaryotes and eukaryotes? Make a schematic illustration.

8. Why are eukaryotes often so more complex in their ways of managing hereditary information?

9. How does translation differ between eukaryotes and prokaryotes?

10. How can the difference be utilized in the battle against infective diseases?

11. What is the general principle in the identification of potential antibiotic targets in prokaryotic pathogens?

12. Apparently, the DsRed2 protein gene used in the first practical contains “a number of silent base-pair changes”. What are they and why are they made?

13. The DsRed protein gene was cloned from an ocean-dwelling coral animal. How must such genes be modified in order to be fully functional in bacteria?

Self-study questions for cell structure practical

  • Go through the complete contents of the first laboratory compendium, including any notes you made in the laboratory. Have you understood what the different functional parts of the plasmids do in the cells?

  • Continue your studies around the DNA lectures, using your lecture notes, powerpoints and the Alberts.

  • Rehearse the contents on the genetics of prokaryotes using lecture notes, powerpoints and the Alberts.

  • Go through all the material for signal transduction including signal transduction and gene regulation.

Look at the picture 1-31 in Alberts and make a list of all the different structures indicated in the picture. Note briefly in the list what or which functions the structures have Use the index in Alberts to find the structures. Even the glossary in the end of the book may be useful.

Cell cycle questions

1. Give examples of cell types (in the human body) grow fast and give some examples of cell types in the body that do not grow nor divide often.

2. Why do the cells require such complicated machinery for regulating the cell cycle?

3. Draw a schematic picture of the cyclin-cdk-system and relate the amount of cyclin in the cell to the different phases of the cell cycle.

4. How is the beginning of the M-phase regulated?

5. What kind of checkpoints do cells use?

6. Is it possible that there are more checkpoints that we haven’t discovered yet? Can you think of possible checkpoint candidates?

7. In chemotherapy against cancer, specific drugs are used to battle cancerous cells. What kind of cell cycles would cancer cells typically have?

8. Chemotherapy causes many cancer patients to loose their hair. Why is that?

Discussion 3 without teacher support

For this discussion no special rooms have been booked; it is up to the groups to decide how and where they will work. Remember that this is a very good opportunity to train leadership, teamwork and organisation skills which are all very important for you future career, whether you are aiming for a career in academia or the pharmaceutical industry.

The use of fluorescent proteins is a very important part of methodology in cell biology. In this week’s practical, you will yourself be using these tools to study eukaryotic cell structure and function. In this discussion, we will study the examples of fluorescent protein studies described in Alberts.

1. How can GFP genes be used to study gene expression (or promoter activity). Draw a schematic illustration on how such a construct would look like.


2. How can GFP genes be used to study the localication of different proteins in the cell? Draw a schematic illustration of such a construct.


3. What is meant by “a fusion protein”? How can such fusion proteins be made? (p 518-519, this is called “tagging” on the page). Again, draw a schematic illustration.

4. How would you make construct that specifically directs a GFP construct to the mitochondrion?

5. How can GFP used to study the synthesis and transport of specific membrane proteins in the cell? Again, make a schematic illustration.

6. Give more examples of functions, processes or structures that could be studied in the cell using variants of GFP proteins.

7. What are the primary advantages of fluorescent proteins in cell biological research?

Discussion 4 with teacher support

In this discussion, the lectures on signal transduction, cell biology methods and intracellular transport will be discussed. Again, one teacher helps two rooms of students and divides the time evenly.
Signal transduction questions

1. Define the following forms of signalling and describe where and when such signalling could occur:

  • Contact-dependent
  • Paracrine
  • Synaptic
  • Endocrin
2. What are the major types of receptors? What are the principal differences in how they work?

3. What is the role of second messengers in the cell?

4. The following types of protein have been described for signal transduction pathways. What are their functions?
  • Amplifier proteins
  • Transducer proteins
  • Bifurcator proteins
  • Integrator proteins
5. What is meant by desentizising? Why is it so important?

6. Give examples of the following types of receptors:
  • Ion-channel linked
  • G-protein linked
  • Enzyme-linked
7. Signal transduction pathways can change the metabolism or function of the cell very rapidly, or more slowly. How is this achieved?

Cell biology methods

1. What is meant by primary and secondary cell cultures?

2. How can cells be cultivated? What kind of special requirements do they have?

3. Can cell cultures be contaminated (with pathogens)? How can this be detected?

4. In the course practical, cells are transfected using a chemical. Discuss alternative ways of modifying organisms genetically.

5. What is a FACS? How are they used in cell biological research?

6. What is a gene knock-out? How are they used in biomedical research?

7. What is meant by in-situ hybridisation? For what purpose are they done?

8. What is meant by a reporter system? Give examples.

Questions on intracellular transport

1. Why is it important for the cell that there are different compartments?

2. Why is there such a huge area of intracellular membranes in the eukaryotic cell?

3. How can different proteins be directed to different compartments or to the cell surface (There are at least two different ways.

4. One type of compartment in the eukaryotic cell is very different from all the others. Which one is it? How do we know that it is different from all others?

5. What are the major functions of the ER?

6. What are the major functions of Golgi?

7. Lysosomes?

8. Peroxisomes?

9. What are endocytosis and exocytosis?

Lab discussion 5 with teacher support

This discussion is devoted to developmental biology – note that the your work on the developmental biology lab will also be discussed here according to the instructions in the lab.

1. What are the principal conceptual differences between meiosis and mitosis?

2. What is a cross-over? What is their significance?

3. When does meiosis happen in a woman? In a man?

4. What is a meiotic disjunction? What can happen as a result? Examples?

5. Explain the following concepts:

  • Totipotent cells: give an example
  • Pluripotent cells: give an example
  • Unipotent cells: give an example
6. What happens in implantation?

7. What happens in gastrulation?

8. What happens in neurulation?

9. How long is the embryonic period in humans? What happens then?

10. How long is the fetal period? What happens then ?

11. The postnatal period? What happens then?

12. Why is it that the embryo or the foetus is so sensitive to teratogenic substances?

13. What is a stem cell?

14. Where can they be found?

15. How long has stem cell therapy been performed in Sweden? (Approximately, note that this is a trick question.)

16. Many researchers dream of using stem cells to repair damages to tissues or organs. How could this be done?

17. What is meant by “tissue engineering”?

18. What is meant by “reproductive cloning”?

19. What is meant by “therapeutic cloning”?

20. Stem cell research is partially banned in some countries (e g research on embryonic stem cells in the United States). What king of ethical problems does stem cell research pose?

21. Describe how a morphogen is thought to work. Give an example.

22. Describe how sequential induction is thought to work.

23. List two (or more) characteristics of chick that make it an advantageous or disadvantageous system in which to study development (two pros, two cons). List two characteristics of mouse that make it an advantageous or disadvantageous system in which to study development (two pros, two cons).

24. List five different things in cell biology that we still do not know, likely to give a fast and easy Nobel prize.

Cellslöjd – Cell crafts for the integrative project

This two-day project is part of the integrative project that spans through the course. The idea is to build and present physical models of different structures and functions in the cell (eg the cell skeleton, the Golgi, ER, surface structures) and relate these to different types of diseases. Materials are supplied by the teachers. The experiment is conducted in a specially designed learning environment at KI (Strix). The unit includes introductory lectures, work in groups to build models plus interactive student and teacher presentations. A separate instruction will be provided

Topic revision: r5 - 2012-03-16 - MattiNikkola