Self-study questions

Introduction work with self-study questions Cell and Molecular Biology

• Our goal is to prepare you for a successful career in biomedical technology. This compendium has been designed keeping this goal in mind.
• This compendium is NOT a list of questions that will be asked you in the final examinations, although some of the questions may be the same. Please do not be fooled into thinking that memorizing model answers is a good way of learning something. It may help you to drag yourself over the pass-point in the final exam, but it will definitely not aid you in understanding biomedical technology. Superficial learning leads to superficial knowledge. True learning requires work (thinking). No pain, no gain; easy come, easy go.
• This is an advanced course since you will be developing and working with advanced technology. Thus there are no model answers in this compendium – although most of the answers should be found in the book. Moreover, we supply discussion hours with teachers to go through the questions where you require help.
• Working with questions and problems is an efficient way of learning. Even more so if you work together with somebody. Perhaps you can organise a study group with people from the course? You can even collaborate with somebody by making up and exchanging questions.
• Think about the basic questions in all learning.
  • What? (Vad)
  • How? (Hur?)
  • Why? (Varför?)
  • How do we know it? (Hur vet man det?)
• Which do you think is the most important question?
• These questions have been written in English but of course you should be free to think and discuss them in any language that you wish. Research on bilingual education shows that 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.

Make an inventory

Study the schedule of the course and the reading assignments for the textbook. Study the way Alberts is constructed and remember that any textbook is a method. 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 on pages G:1-36 and a complete index in the end. Finally read pages 3-44 from Alberts. Don’t forget to use the reading specifications (läsanvisningarna) for important concepts.

Make a study plan

Most successful projects are successful because there has been some level of planning involved. Consider this course a project – a rehearsal for what you will be doing in a company in the future. Consider the task (the learning goals) of this course, the assigned reading material, the available time, and your own priorities and make a study plan for the spring. It does not have to be extremely detailed, the main thing is that works for you. Notice that planning even makes life less stressful.

Introduction

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?

Molecular biology questions

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 their 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.

Cell biology questions

Take a 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 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. What is a gene knock-out? How are they used in biomedical research?
5. What is meant by a reporter system? Give examples.

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?

Cell cycle questions:

1. Give examples of cell types (in the human body) that have very long cell cycles and of cell types that have very short cell cycles, dividing 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?

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. 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?
4. What are the major functions of the ER?
5. What are the major functions of Golgi?
6. Lysosomes?
7. Peroxisomes?
8. What are endocytosis and exocytosis?

The cell skeleton

Draw a schematic illustration of the cell, and try to find answers or good guesses to the following (or use the book to give the answer) in preparation for the lecture. How can eukaryotic cells move? Why do eukaryotic cells move? Can you think of situations where cells move in the human body? What determines the size and the shape of a cell? What is a skeleton? Why do different organisms have skeletons? Is it correct to call the cell skeleton a skeleton? What are the principal components of the skeleton? What are their different roles? What is a “molecular machine”? Can you give examples? Or a motor protein?

The surface of the cell; junctions and the matrix

What surrounds cells in the human body. What fills up the space in between the cells? What are the principal components? What are their functions? Are there tissues with very little space between cells? Give example of a tissue with very much space between cells. How are cells connected to each other? What are the principal types of connections? How do these different types of connections differ functionally?

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 desentisising? 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?

Questions on developmental biology

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?

Questions on bioinformatics

1. How would you define bioinformatics now?
2. Making a very educated guess, how would you define bioinformatics in the year 2015?
3. If you were given a file with “raw” DNA sequence from the human genome (a few Megabasepairs), how would you go about finding if there are any “genes” on the chromosome?
4. If you find any candidates for genes in this stretch of DNA, how would you verify that they really are active genes?
5. Can you make any educated guesses about the functions of the putative genes found? How would you do it?
6. Starting from the other end – if somebody gives you the amino acid sequence of a protein, can you figure out what the gene sequence for making such a protein would be?
7. How does one find out if a new gene for a protein has any “relatives”?
8. Why are chromosomes so “messy” (seemingly at least), full of repetitive sequences and other material and so few genes?
9. What kind of databases are there in bioinformatics?
10. If you had to choose, which would be the three most important methods for a novice bioinformatician to master?

Questions on immunology and microbiology

1. What is the basic structure of the antibody?
2. What are the major functions of an antibody?
3. Why are there different types of antibodies?
4. How do cells produce the huge variety of antibodies with different specificities?
5. Vad menas med medfött och specifikt immunitet?
6. Hur vet kroppen att någonting är främmande eller farligt?
7. Hur vet kroppen vad som är kroppens egna celler eller proteiner?
8. Vad är “inflammation”?
9. Ge exempel på sjukdomar med koppling till inflammation.
10. Vad menas med “autoimmune sjukdomar”? Ge exempel?
11. Hur kan antikroppar användas inom diagnostik?
12. Vad menas med monoklonala antikroppar?
13. Vad är allergi?
14. Hur fungerar det lymfatiska systemet?
15. Vem beskrev det först?
16. Hur lär immunsystemet att minnas – t ex virus eller bakterier?
17. Hur länge kan immunsystemet minnas?
18. Vad innebär en vaccinering?
19. Vilka sjukdomar kan man inte vaccinera sig mot?
20. Kan man vaccinera sig mot annat än smittsamma sjukdomar?
21. Vad menas med “patogenicitet”?
22. Vad menas med “virulens”?
23. Vad menas med bakteriostatiska och bakteriocidala medel?

The really good questions List five different things in cell biology that we still do not know, likely to give a fast and easy Nobel prize, or a novel biomedical technology innovation.