College aantekeningen

Experimental Cell biology I minor lecture notes 1-9

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Vrije Universiteit Amsterdam (VU)

These are my lecture notes from all the lectures (except the lecture about the assignment). It contains some pictures from the powerpoint and elaborate explanation of the subjects. Goodluck!!

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Geschreven in 2022/2023
Type College aantekeningen
Docent(en) Dr. dirk bald
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Lecture 1 – cell biology (cells)
Cells come in different shapes and sizes
- They have different aspects
o They are membrane-enclosed unit of life
o Have metabolism = each cell has a different way it metabolizes
o Growth and division
o Response to environmental signals, internal and external communication

Cell biology has different topics. The questions that are always asked are
- What happens? In and outside a cell
- Which factors are involved?
- Why does it happen? – the cause and consequence
- Where does it happen in the cell?
- Can we modify/ manipulate cellular processes?

Cell biology relates to many other fields = so it is interdisciplinary

- Bio-medicine = to understand why certain diseases occur etc.

DNA = genetic material
Proteins = the workhorses
Metabolites = molecules produced or altered by cell

! there are alot of feedback moments in between all of these
which is very important !

,Different cell types
1. Prokaryotic cell
o Small: 1 – 5 µm (it is good to know the size of
things to know which technique is best to use
in research)
o Typically single cells
o No internal membrane compartments
o Very flexible metabolism

2. Eukaryotic cell
o Larger than the prokaryotic cell: 20 – 50 µm
o Many are milty-cellular
o Has membrane-enclosed compartments
 Nucleus
• The place for DNA synthsis and storage of the DNA
• RNA synthesis also happens = specifically in the nucleolus
o The nucleolus
1. is the site of RNA and ribosome synthesis
2. It is involved in protein quality control
• Chaperones will fold the denatured proteins
again when misfolded

Frottin et al. 2019
- They stained the nucleolus of a certain area. They used
markers for this
- A protein is then put into the nucleolus labeled with
GFP (a dye)
- A heat system destabalizes the protein
- This destabalized protein moves to the previously
marked area in the nucleolus to be refolded

• The nucleus is surrounded by a phospholipid membrane
• The membrane has nuclear pores for transort between the cytosol
and the nucleus

, Endoplasmatic reticulum (ER)
• Large part of the cell
• For moving/ modification/ transport/ sorting of proteins
• Also closely connected to protein synthesis
o Specifically the proteins that enter the cell = the first station
they encounter is the ER
• Has many functions
o Improtant role in division of mitochondria
1. The ER mediates this process
2. It forms a clamp around the mitochondria at the
place it needs to split

Glycosylation = post translational
modification – different types of glycans
 Golgi apparatus are covalently attached to proteins
• Membrane system
• On the route, after the ER, the proteins encounter the golgi
apparatus. It mofidies the membrane proteins
o In particular glycosylation happens of the proteins
• Sorting and transport of proteins happens here as well
o The transport happens from and within the golgi by
transport vessicles
o The golgi apparatus has two sides = Cis- and trans- side

 Mitochondria
• It produces ATP = energy metabolism
• Fatty acid oxidation takes place there
• Functions = ATP prduction and plays a role in the cytric acid cyle

 Lysosome
• Very small: several 100 nm
• Contains hydolytic enzymes = break down large molecules into
smaller ones
• Functions
o Degredation and signaling processes
1.> Involved in autophagy (settembre et al, 2013) = eats
up proteins/other stuff to degrade it
o Secretion

 Transport vessicles
• They are used for transport between compartments
• Are membrane enclosed vessicles
• Smaller than other organelles
• Crucial for transport material between two comparments in a cell
• Closely related to the ER and golgi

,  Cytoskeleton
• Functions
o It is structuring the cell
o Important for movement of the cell
o Transport in the cell
• Fillaments = are protein based structures that all have the functions
that are stated above
o Thick = microtubule
o Thin = Actin
o Intermediate = keratine

 Chloroplast
• Involved in photosynthesis = energy from the sun --> ATP

 Cytosol
• Water based gel
• Contains a lot of molecules = macro and micro
o Which means that the cytosol is very crowded
1.> Consequence = metabolites do not have a lot of
space left
2.> The metabolites are very close to eachother so the
effective concentrations and reaction rates are
higher
• Many metabolic steps happen in the
cytosol

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