Molecular Biology of the Cell

6 EC

Semester 1, period 1

5234MOBC6Y

Owner Master Biomedical Sciences
Coordinator dr. M.E. Stam
Part of Master Biomedical Sciences, track Oncology, year 1Master Biomedical Sciences, track Infection and Immunity, year 1Master Biomedical Sciences, track Cell Biology and Advanced Microscopy, year 1Master Biomedical Sciences, track Biochemistry and Metabolic Diseases, year 1Master Biomedical Sciences, track Experimental Internal Medicine, year 1Master Forensic Science, year 2

Course manual 2016/2017

Course content

The course provides fundamental knowledge on molecular and cellular Biology. The subjects addressed are the following:

  • Basic knowledge of DNA, genomes, genes, gene regulation, transcription, RNA, translation, gene regulation, the cell cycle.
  • Up-to-date molecular techniques such as High-throughput sequencing, Microarray analysis, Chromatin immunoprecipitation, Bisulfite sequencing, proteomics.
  • Cell culturing techniques, cell separation and fluorescence microscopy analysis.
  • Basic Biotechnology: genetically modified organisms, such as bacteria, yeast, plants and animals.
  • Basic knowledge on the regulation of gene expression and genome function by chromatin structure, DNA methylation, RNA interference and long non-coding RNAs.
  • Basic knowledge of protein synthesis, protein targeting, protein trafficking and cell signaling.

Study materials

Literature

  • Molecular Biology of the Cell, Alberts et al., Taylor & Francis Inc  (6th edition; Chapter 2-8).

  • Recommended: Epigenetics, Allis D., Cold Spring Harbor Press, (2nd ed, 2015)

Syllabus

  • Hand-outs & papers posted on Blackboard

Software

  • CLC DNA Workbench (licenced/provided by UvA)

Objectives

The topics studied in this course are molecular and cellular processes underlying gene regulation, epigenetic mechanisms, RNA transcription, protein synthesis, protein targeting and trafficking, the cell cycle and cell signaling. 

At the end of the course, the student should be able to:

  • Explain basic knowledge on molecular and cellular processes
  • Interpret figures, formulas and schemes on molecular and cellular processes 
  • Apply basic knowledge on molecular and cellular processes on data, figures, formulas and schemes provided
  • Sketch molecular and cellular processes textually and in drawings
  • Analyse datasets using basic web tools for genomic and proteomic data 
  • Interpret data obtained by using basic web tools for genomic and proteomic data 
  • Interpret literature on molecular and cellular processes in a critical manner 
  • Formulate knowledge on molecular and cellular processes in a structured and logic manner
  • Present knowledge on molecular and cellular processes in a structured and logic manner to peers
  • Discuss presented knowledge on molecular and cellular processes in a critical manner

Teaching methods

  • Lecture
  • Computer lab session/practical training
  • Presentation/symposium
  • Self-study
  • Working independently on e.g. a project or thesis
  • Supervision/feedback meeting
  • Seminar
  • At the lectures the basic knowledge on molecular and cellular processes is provided, explained and discussed. Students are involved in the lectures by asking questions to the students. 
  • At the tutorials (seminars) the students will apply the knowledge obtained in the lectures by answering old exam questions and questions designed specifically for the tutorials. The students will have to interpret figures, formulas and schemes during the tutorial and sketch molecular and cellular processes in drawings. The answers given by students are discussed by the lecturers in an interactive manner. 
  • In computer practicals students apply acquired knowledge, learn to use basic web tools for genome and proteome analysis and interpret the results obtained.
  • The knowledge discussed in the lectures and practiced at the tutorials is the basis for an assignment that aims to train students in a critical evaluation of literature, in formulating knowledge on molecular and cellular processes in a structured and logic manner in an essay. They in addition learn to collaborate in small groups. 
  • The knowledge acquired when writing an essay is presented to an audience of peers. Through presentation of their topic, questions asked by their peers and feedback of lecturers, students become acquainted with the scientific method.
  • The feedback the students receive on their draft and final versions of the essay and presentation stimulate them to reflect and improve their performance. 
  • During self-study the students learn to memorise and comprehend the knowledge provided.

Learning activities

Activity

Number of hours

Lectures

26

Computer practicals

8
Tutorials 6
Digital test 1

Feedback Discussion Assignment 

1

Presentation Assignment

4

Question hour

3

Exam

3

Self study

116

Total 6 EC x 28 h

168

 

Attendance

The programme does not have requirements concerning attendance (OER-B).


Additional requirements for this course:

Additional requirements for this course:

Attendance at computer practicals, the digital test, and at feedback moments and presentations of the Assignment is mandatory.
Attendance at lectures and tutorials is highly recommended.

In case of serious issues contact the course coordinator.

Assessment

Item and weight Details

Final grade

50%

Tentamen

10%

Digital test

90%

Final exam

Must be ≥ 5.5, Allows retake

40%

Assignment

50%

Literature essay

Must be ≥ 5.5, Allows retake

35%

Oral presentation

Must be ≥ 5.5

15%

Discussion essay topic

Must be ≥ 5.5

10%

Computer practical

Must be ≥ 5.5

In case of serious issues, please contact course coordinator.

Inspection of assessed work

The manner of inspection will be communicated via the lecturer's website.

Assignments

Literature essay

  • Write an essay on a given topic (groups 2-3 students).

Oral presentation

  • Present essay topic to peers (groups 2-3 students).

Discussion essay topic

  • Discuss own and one other essay topic during presentations.

Onderstaande opdrachten komen aan bod in deze cursus:

  •    Naam opdracht 1 : beschrijving 2
  •    Naam opdracht 2 : beschrijving 1
  •    ....

Fraud and plagiarism

Dit vak hanteert de algemene ‘Fraude- en plagiaatregeling’ van de UvA. Onder plagiaat of fraude wordt verstaan het overschrijven van het werk van een medestudent dan wel het kopiëren van wetenschappelijke bronnen (uit bijvoorbeeld boeken en tijdschriften en van het Internet) zonder daarbij de bron te vermelden. Uiteraard is plagiaat verboden. Hier wordt nauwkeurig op gecontroleerd en streng tegen opgetreden. Bij verdenking van plagiaat wordt de examencommissie van de opleiding ingeschakeld. Wanneer de examencommissie overtuigd is dat er plagiaat gepleegd is dan kan dit maximaal leiden tot een uitsluiting van al het onderwijs van de opleiding voor een heel kalenderjaar. Zie voor meer informatie over het fraude- en plagiaatreglement van de Universiteit van Amsterdam.www.uva.nl/plagiaat

Course structure

Weeknummer Onderwerpen Studiestof Deadline
1  Lecture Introduction to the course: all ins and outs of the course are being communicated and the groups for the assignment are being formed    
1  Lecture Molecular Biology    
1 Lecture Gene expression & regulatory sequences    
1 Lecture Transgenesis    
1 Lecture Introduction into DNA methylation & the DNA methylation analysis computer practical    
1 Tutorial on lectures on Molecular Biology, Gene expression & regulatory sequences, and Transgenesis  Lectures indicated  
1 Computer practical: Basics of Molecular Biology & DNA methylation analysis     
2 Lecture DNA methylation    
2 Lecture Histone modifications    
2 Lecture Histone variants    
2 Lecture non-coding RNAs     
 2 Tutorial on lectures on DNA methylation, chromatin structure and nc-RNAs    
 2 Computer practical: gene structure analysis    
 2 Assignment: Hand in draft essay     16:00, Wednesday 2nd week
 2 Assignment: Oral and written Feedback on the draft essay    Friday 2nd week
 3 Digital test: testing the knowledge obtained in lectures in the first 2 weeks    
3 MSc Internship market    
3 Lecture Protein synthesis, structure & purification    
3 Lecture Membranes & proteins    
       
       

Timetable

The course schedule can be found at https://datanose.nl/

Additional information

It is recommended to perform the background knowledge test available at the Blackboard site a couple of weeks before the start of the course. If the test indicates a gap in your active knowledge you still have time to refresh your memory. The test does not count for your final mark. The course is a full-time course.

Contact information

Coordinator

  • dr. M.E. Stam