Summary Class notes - Cell biology - Histology

Course
- Cell biology - Histology
- Verheijen; van Weering; Luirink; Smit; Molenaar
- 2018 - 2019
- Vrije Universiteit Amsterdam
- Biomedical Sciences
286 Flashcards & Notes
3 Students
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Summary - Class notes - Cell biology - Histology

  • 1542841200 Cells and organelles (van Weerink)

  • What are characteristics of a cell?
    • is the essential building block of all life on Earth.
    • has a limiting membrane (inside/outside compartments.
    • contains biomolecules (e.g protein/RNA/DNA).
    • is an autonomous unit in performing a function.
    • can respond & adapt to stimuli.
    • can (often) reproduce itself.
  • What are the basic ingredients of a cell?
    • DNA: deoxyribonucleic acid the language of genes
    • Proteins: form code to function
  • What are the groups that a cell can belong to? What are the properties of these groups?
    • Bacteria: no nucleus or other organelles
    • Archaea: no nucleus, often extremophiles
    • Eucaryotes: nucleus and other organelles, sometimes multicellular life forms.
  • What are the different microscopy methods
    • Light microscopy (LM)
    • Fluorescence microscopy
    • Electron microscopy (EM)
  • What are the advantages of EM over LM?
    • Superior resolution (up to 0.5 nm!, atoms!)
    • Visualise the whole cell, not only a fluorescent probe (e.g. GFP).
    • Huge magnification range (30x-300.000x: 104)
  • What are the disadvantages of EM compared to LM?
    • Requires fixation of cells (operates under vacuum).
    • Only small pieces of tissue can be imaged.
    • Time-consuming method
  • What is the structure of a nucleus?
    A nucleus has a roundish structure with some loops.
  • What is the nucleolus?
    The nucleolus actively transcribes DNA into RNA.
  • Why does a nucleus show as a darker circle under a microscope?
    A nucleus shows as a darker circle under a microscope because a lot of proteins are found in the nucleus.
  • What is the nucleus pore responsible for?
    A nucleus pore is responsible for transport of proteins and RNAs in and out of the nucleus.
  • What do you see here?
    A nucleus
  • What is chromatin?
    Chromatin is a complex of DNA and proteins that forms chromosomes. It is the storage of DNA in chromosomes.
  • What is the function of the endoplasmic reticulum (ER)?
    Translation of RNA to a protein.
  • What is the structure of the ER? Why is this?
    The structure is like a fishnet, this increases the surface so proteins can be transported through the cell.
  • What is rough ER?
    Rough ER is the the ER where ribosomes are attached.
  • What do you see here?
    Endoplasmic reticulum (ER).
  • What is the function of the golgi apparatus?
    Protein modification and protein sorting.
  • What is the structure of the golgi apparatus?
    The golgi apparatus is like a fishnet, this increases the surface so proteins can be transported through the cell
  • What do you see here?
    The golgi apparatus.
  • What is the function of the mitochondria? How does it fulfill this function?
    The mitochondria is the energy supply of the cell. Burning glucose yields energy in the form of adenosine triphosphate (ATP).
  • Why do mitochondria have their own DNA?
    Mitochondria have their own DNA because they are derived from bacteria.
  • What do you see here?
    Mitochondrium.
  • What are chloroplasts?
    Chloroplasts are responsible for the energy supply in plants because photosynthesis happens in this part of the cells.
  • Do plants only have chloroplasts or are mitochondria also present?
    Plants still need mitochondria to burn the glucose provided by in photosynthesis.
  • What do you see here?
    A chloroplast.
  • Is cytoplasm fluid?
    Cytoplasm is not fluid, but a jelly matrix of proteins
  • What are the processes that occur in cytoplasm?
    • Transport
    • Protein synthesis
    • Protein break-down
    • Signal transduction
    • Membrane fusion
    • Ionic homeostasis
  • What is the function of the cytoskeleton and where does it occur?
    The cytoplasm contains the cytoskeleton that is responsible for the form and transport of the cell. 
  • What are the three types of filaments that the cytoskeleton contains?
    • Microtubules
    • Intermediate filaments
    • Actin
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What is the function of chaperone proteins in the ER?
Chaperone proteins in the ER bind to proteins that didn't bind properly.
What is the process of growth factor signaling?
A TGF-β binds to a TGF-β-receptor. The tail gets activated because of phosphorylation. One SMAD gene regulatory protein binds to get phosphorylated, then it binds to another SMAD gene regulatory protein and it becomes activated. When it's activated it goes into the nucleus and the DNA is transcribed into RNA.
What is the process of cytokine signaling?
A cytokine binds to cytokine receptors, this causes a conformational change. The tyrosines come into contact and phosphorylate each other. When activated the tail also get phosphorylated. Two STAT gene regulatory proteins can bind to this phosphor on the tails. The STAT gets activated by binding to each other. It goes into the nucleus and DNA is transcribed into RNA.
How is the order of the proteins in the Ras-Map-kinase pathway defined?
Introducing specific mutations.
Mutations made in different proteins of the signaling cascade help to dissect their role. Some of the mutations may occur naturally in the cell leading to highly disturbed signaling, that might lead to cell division (cancer).
Describe the Ras-Map-kinase pathway.
After the RTK is activated an adaptor protein will bind to it. The RAS-activation protein binds to the adaptor protein. RAS-activation protein activates the Ras protein by changing bound GDP to GTP. Activated Ras protein activates MAP kinase kinase kinase. With help of ATP, activated MAP kinase kinase kinase is formed into activated MAP kinase kinase. Again with the help of ATP, activated MAP kinase kinase is formed into activated MAP kinase. Activated MAP kinase phosphorylates various downstream signaling or effector proteins.
What is the process of activation of receptor tyrosine kinases (RTKs)?
A signal molecule in the form of a dimer binds to the extracellular domain of the RTK. The kinase domains on both receptors get into contact with each other. This activates the kinases to phosphorylate the adjacent tail on several tyrosines. Each phosphorylates tyrosine serves as a specific docking site for a different intracellular signaling proteins, which then helps to relay the signal to the cell's interior.
Which two signaling pathways are shown here?
G-protein-coupled signaling and ion-channel-linked signaling.
What is the process of gene transcription activation caused by adrenaline?
Adrenaline binds to a receptor protein. The α-subunit gets activated and binds to adenylyl cyclase which also gets activated by this binding. ATP is now converted into cyclic AMP. cAMP activates PKA. The active PKA moves into the nucleus and phosphorylates specific transcription regulators. Once phosphorylated, these proteins stimulate the transcription of a whole set of target genes.
What is the proces of glycogen breakdown that starts with a G-protein-coupled receptor?
The hormone adrenaline binds to a protein receptor. This activates the G-protein. The α-subunit binds to adenylyl cyclase which is then activated. ATP is now converted into cyclic AMP. cAMP activates PKA. The active PKA plus ATP activates phophorylase kinase. Active phophorylase kinase plus ATP activates glycogen phophorylase, which breaks down glycogen.
How is cyclic AMP synthesized and degraded?
Cyclic AMP is formed from ATP by a cyclization reaction that removes two phosphate groups from ATP and joins the "free" end of the remaining phosphate group to the sugar part of the AMP molecule The degradation reaction beaks this bond, forming AMP. Cyclic AMP is degraded by cyclic AMP phosphodiesterase.