Cellbio

Name a microscopic method that is suitable in terms of resolution to make larger protein molecules visible

What methods can you use to visualize lipid rafts

Which method allows the elucidation of the molecular structure of proteins at atomic resolution and in what form must the protein be available for this investigation?

Which method can you use to fractionate cell organelles and according to which physical size are the organelles fractionated in this method?

Which chromatography method does not separate on the basis of affinity to the chromatography matrix

According to which physical quantity are proteins essentially separated in SDS gel electrophoresis?

Which electrophoresis technique can you use to separate individual proteins from highly complex mixtures? Which two physicochemical parameters of the proteins are decisive for the separation result?

Which method can you use to specifically visualize certain proteins after electrophoresis?

How can you label a protein to study its behavior in a living cell under the microscope?

Which method can be used to specifically repress the expression of certain proteins without manipulating the genome (no abbreviation)?

How is the unlimited cell division capacity of the antibody-producing cells achieved in the production of monoclonal antibodies?

Which metabolic pathway is blocked during the production of monoclonal antibodies in order to select for the growth of antibody-producing cells in cell culture?

Which two substances do you have to supply to the cells under blockade conditions of this metabolic pathway so that they can still grow?

Why are monoclonal antibodies produced using mice and not rabbits?

You want to use immunofluorescence microscopy to detect the LDL receptor and the mannose-6-phosphate receptor in two separate approaches with polyclonal antibodies against the corresponding proteins.

In which approach do you need to add detergent to the fixative solution?

What technique can you use to use antibodies to purify your antigen?

When fixing cells for immunofluorescence microscopy, what type of agent do you add to permeabilize the cells?

What is the purpose of permeabilization?

Why are cells or tissue sections often treated with detergents during immunofluorescence microscopy?

What is the advantage of indirect immunofluorescence microscopy over direct immunofluorescence microscopy?

Which two parameters determine the resolution in microscopy?

What is the approximate lateral resolution limit for light microscopy?

Why do you achieve a much higher optical resolution with electron microscopy than with light microscopy?

Name a method for detecting protein interaction between two proteins

What type of agent (collective term) do you generally need to isolate a membrane protein and what is its function?

Which method can you use to detect the mobility of a protein within the membrane?

Which method can you use to isolate individual cells directly from a tissue bandage for further cell biological or biochemical analysis?

Which method can you use to sort different types of single cells based on the presence of specific marker proteins?

Which 3 classes of membrane lipids do you know?

Name the 3 types of membrane lipids shown and circle the part of each molecule that has hydrophilic properties

Name the sites of synthesis of cholesterol, phosphoglycerides and sphingolipids

What are the 3 basic building blocks of phosphoglycerides?

What is the difference between glycosphingolipids and sphingomyelin?

Which property of membrane lipids is responsible for the structure of biological double membranes?

Which protein structure or protein structures can occur in transmembrane proteins within a membrane passage? amphipathic properties

Name 5 fundamentally different ways in which peripheral membrane proteins can associate with the membrane

Which two structurally different types of long-chain lipid residues can occur as lipid anchors when peripheral membrane proteins bind to the membrane? Name either the generic term that describes the lipid type or give an example of each

Name three functions of the glycocalyx

What type of membrane lipids preferentially accumulate in lipid rafts?

Name one protein and one lipid type typically associated with rafts.

As a precursor for which molecules does the body need cholesterol as a basic building block?

Which two enzymes catalyze the thermodynamically unfavorable transverse change of a membrane lipid from one membrane sheet to the other in biological membranes?

Name the 5 electron microscopically distinguishable forms of endocytosis vesicles

Which forms of coated vesicles do you know, in which transport pathways do they occur and which small GTPase is involved in the strangulation process?

How can you experimentally inhibit GTPases?

Which types of coated vesicles are not formed at the plasma membrane?

Which types of coated vesicles are not formed at the Golgi apparatus?

What is the function of GTP cleavage by Sar1 or ARF1 after the pinching off of a transport vesicle?

What is the name of the molecular switch protein that regulates both the assembly and disassembly of the coat when an ER vesicle is pinched off? Which molecule is converted in the process?

What is the name of the regulatory protein that regulates both the assembly and disintegration of the coat when an ER vesicle is pinched off? Which other regulatory protein determines which target membrane the vesicle can fuse with?

What is the name of the molecular switch protein that regulates both the assembly and disassembly of the coat when a Golgi vesicle is pinched off? Which molecule is converted in the process?

Give an example of a transport material that is taken up from the blood via receptor-mediated endocytosis and the characteristic coat protein involved in the formation of endocytosis vesicles

In receptor-mediated endocytosis, which proteins are mainly responsible for a) the invagination process and b) the vesicle pinching process?

Which endocytosis process requires dynamin?

Name a plasma membrane protein that can mediate the phagocytosis of bacteria

Which protein is involved in all endocytosis processes

Proteins from which protein family are involved in both vesicle truncation and vesicle fusion? Give one example of each

Give the names of two nucleotide-cleaving proteins that can occur simultaneously on the vesicle membrane and the nucleotide

which interaction between which proteins is primarily responsible for ensuring that

vesicles a) fuse with the target membrane and b) which interaction ensures that they fuse with the correct target membrane?

to b)What is the name of the tertiary structure that the proteins involved in this process form during vesicle fusion?

Which protein (name) regulates assembly and dissassembly of COPII vesicle shells and where are these vesicles formed?

Which step in vesicle transport is inhibited by the addition of NEM (N-ethylmaleimide), and what is the name of the inhibited protein?

What effect does the addition of NEM have on vesicle fusion and how can it be explained?

What is the direct effect of inhibition of the NSF/α-SNAP complex on vesicle transport and how can it be explained?

Why does the NSF/α-SNAP complex need ATP?

How does inhibition of the NEM-sensitive factor (NSF) by the toxin NEM inhibit vesicle transport?

Why does botulinum toxin inhibit vesicle fusion?

Where in the cell does the initiation of translation of a membrane protein take place, and where does that of a mitochondrial protein?

In which compartment of the cell does the initiation of translation of a secretory protein take place and where does that of a peroxisomal protein take place? where in the cell does the initiation of translation of a membrane protein take place and where does that of a mitochondrial protein take place?

To which group do the proteins that regulate the assembly and dissassembly of vesicle coats belong and which substrate do they convert due to their enzymatic activity?

What manipulation would you have to perform to experimentally force a cell to secrete a cytosolic protein?

What manipulation would you have to perform to experimentally force a cell to accumulate a normally secretory protein in the ER lumen?

Where (compartment) is the C-terminus of a type I membrane protein located a) immediately after synthesis, b) during vesicle transport and c) at its final destination, the plasma membrane?

You are investigating the transport of a type II membrane protein. a) In which compartment is the C-terminus located during transport in the vesicle, b) where is it located after fusion of the vesicle with the plasma membrane?

You have the protein sequence of two transmembrane proteins. What do you need to examine these sequences for to be able to predict whether you have a type I or type II membrane protein?

In a certain protein of the plasma membrane with a membrane passage, the C-terminus is located in the ER lumen. Where is the C-terminus located in the transport vesicle

a) from the ER to the Golgi,

b) from the Golgi to the plasma membrane and

c) after vesicle fusion with the plasma membrane

Name 4 functions of the Golgi apparatus

Which forms of glycosylation of proteins do you know and in which compartment does the cell begin with the respective glycosylation?

To which functional group of which amino acids can sugar chains be attached during glycosylation?

In which compartment does the cell begin glycosylation and to which amino acids are the sugars bound there?

The illustration shows 3 glycosylatable amino acid residues within a polypeptide chain. State the name of the corresponding amino acid and circle the atom to which the sugar molecules are bound during protein glycosylation.

Where does glycosylation take place?

Name 3 forms of protein modification that take place during protein biosynthesis at the rough ER

Which sugars make up the preformed basic sugar scaffold that is attached to proteins synthesized at the rough ER?

From which molecule is the basic sugar scaffold transferred to proteins?

To which family of molecules does it belong?

Name 2 functions of glycosylation of proteins

Where does the formation of disulfide bridges take place during protein processing and what is the name of the enzyme that catalyzes this process?

What reaction conditions (environment) must be present for the formation of disulfide bridges and where in the cell are such conditions present?

Why can't the formation of disulfide bridges take place in the cytosol?

Why do cytosolic proteins have no disulfide bridges?

Name the 4 protein folding components in the ER

What is the functional principle of chaperonins?

What form of intermolecular interactions causes the binding to chaperonins and what is the function of ATP cleavage by chaperonins?

Give 2 examples of protein hormones, two of their main post-translational modifications (glyc, oxide, proteolysis) and the site of their final processing from prohormone to mature hormone and what the final processing step consists of

Which type of vesicle travels between the Golgi cisternae from cis to trans or from trans to cis?

Which coat protein is carried by vesicles that traffic between trans-Golgi and endosomes?

What do vesicles that are transported from the CGN to the ER carry?

Which signal is used to ensure that ER-specific proteins remain enriched there?

Which amino acid sequence signal is used to recognize ER-specific proteins in the cis-Golgi and transport them back to the ER?

Which type of vesicle is involved between the TGN and endosomes, which small GTPase regulates strangulation and which adapter proteins are involved in the formation of the coat?

Name the four different types of coat proteins that occur in transport vesicles

Which envelope protein characterizes the vesicles that transport mannose 6-phosphate receptors from the early endosome back to the Golgi apparatus?

In which vesicle transport process in the cell do retromer-coated vesicles occur?

a) Which 2 chemical reactions take place during the processing of proinsulin to mature insulin? b) Where in the cell do each of these reactions take place?

For each of the 4 types, name the cellular transport process in which it occurs.

Which sorting signal on lysosomal proteins is used by the Golgi apparatus for correct sorting to the lysosome?

Where (organelle and subcompartment) does the formation of the post-translational modification typical for lysosome proteins take place and what is it?

Give an example of transcytosis

Along which cytoskeletal elements does the transport of ER vesicles take place in animals?

Which type of motor protein is most likely to be involved?

a) Along which cytoskeletal elements does the transport of Golgi vesicles with secretory proteins take place and

b) Which type of motor protein is most likely to be involved?

In addition to actin itself, name two other important protein components for the outgrowth of lamellipodia.

Briefly state the function of each of the protein components you have named.

Which dominant cytoskeletal elements and which associated motor protein can you find in flagella?

Which nucleotides cleave dynein and dynamin?

Name the function of the proteins dynein, dynamin and dynactin using one term each.

Explain the origin of the name Dynaktin

Which cytoskeletal filaments can spontaneously assemble from their basic building blocks?

Name a common type of intermediate filament

Which cytoskeletal protein subunits cleave nucleotides in vivo and which nucleotides are these?

Welche Untereinheiten des Zytoskelettproteins spalten in vivo Nukleotide und um welche Nukleotide handelt es sich?

What are the consequences of nucleotide cleavage with regard to the critical concentration?

What requirements must be met for treadmilling with microtubules?

What explains the lag phase in the spontaneous polymerization of actin and tubulin filaments from the basic building blocks?

You carry out an in vitro actin polymerization experiment under 2 different conditions and obtain the result shown below. What distinguishes the conditions in curve a (dark gray) from those in curve b

Regarding the same experiment: Why does the mass of filaments no longer increase after some time under both conditions, but remains constant despite a sufficient amount of ATP?

What is the basic building block of the actin or tubulin filament?

What are the two prerequisites for the formation of an ATP or GTP cap?

To which two superordinate protein families do most actin-binding proteins belong?

Which characteristic and fundamentally different secondary structure feature characterizes the repetitive parts of these two protein families?

What is the consequence of treating cells with latrunkulin/cytochalasin/phalloidin/nocodazole/taxol on filament length? Also indicate the cytoskeletal filament type affected in each case.

What is the molecular cause of rigor mortis?

Name one toxin that leads to the stabilization or depolymerization of actin filaments and one toxin that leads to the stabilization or depolymerization of microtubules

Which substance could you add to an in vitro microtubule polymerization experiment to ensure that the microtubules formed no longer depolymerize even after the GTP has been consumed?

Which 3 types of cytoskeletal motors do you know, with which cytoskeletal elements do they interact and in which direction do they move?

Why do intermediate filaments have no intrinsic polarity?

Which cytoskeletal elements cleave nucleotides and which property is directly regulated by nucleotide cleavage

What is meant by dynamic instability?

Draw schematically an epithelial cell, a freely motile cell and a nerve cell with the position of the microtubule cytoskeleton and the cell nucleus and indicate the position of the ends of the microtubules.

Draw the position of the microtubule cytoskeleton, the cell nucleus and the centrosome in the epithelial cell/free-moving cell/nerve cell shown schematically below and indicate the position of the plus and minus ends of the microtubules.

Which spindle checkpoint protein prevents the activation of the separase as long as the checkpoint is active?

Which proteins serve as molecular switches for the formation of a) filopodia, b) stress fibers, c) lamellipodia and d) to which protein family do they belong?

Name 2 fundamental differences in the mechanochemical coupling between myosin and kinesin motors

Which property of conventional kinesin is responsible for the fact that one motor molecule is sufficient for the transport of a vesicle along a microtubule?

What is meant by processivity in motor proteins?

To which group of ATPases does dynein belong

Which molecular complex is required to bind dynein to the transported material?

Where in the cell is the Golgi apparatus normally located and which protein's activity is responsible for this localization?

Along which cytoskeletal elements does the transport of organelles take place in animals?

Which two fundamentally different types of motor proteins are involved in organelle transport in animal cells?

Which motor protein is responsible for the movement of cilia and flagella?

You carry out an immunofluorescence microscopy experiment with mammalian culture cells and label microtubules with fluorescence-labeled antibodies against EB1 and other-colored fluorescence-labeled antibodies against alpha-tubulin.

a) Where on the microtubules does EB1 staining occur?

b) What does the presence or absence of staining against EB1 tell you about the growth status of the individual microtubules?

Which property regarding their interaction with microtubules is characteristic for microtubule-(+)-end-tracking proteins?

a) Where in the cell do you expect to find the highest concentration of gamma-tubulin and b) what is its function there?

Where on the microtubule and where in the cell is gamma-tubulin located and what is its function?

Which protein complex nucleates microtubules in vivo and where in the cell does it have the highest concentration?

Why does centrosome duplication have to be synchronized with the cell cycle and which defect typically occurs in case of mismatched synchronization?

With which cell cycle phase is centrosome duplication synchronized in most cell types?

When in the cell cycle does centrosome duplication begin in most cells?

Name a process in which the joint interaction of the actin and tubulin cytoskeleton is of crucial importance

Indicate one staining method for visualizing microtubules or actin in a fixed cell preparation using light microscopy.

Draw the position of the 3 main F-actin structures discussed in the lecture in the moving cell shown in the diagram and name them (filopodia, stress fibers, lamellipodia)

Which proteins serve as molecular switches for the formation of the structures you have drawn and to which protein family do they belong?

In addition to actin itself, name two other important protein components for the outgrowth of lamellipodia

Briefly name the function of each of the two protein components you have named

Where in the ATP cleavage cycle does the power stroke occur with conventional kinesin or with myosin?

Which actin filament nucleator proteins/protein complexes do you know and in the formation of which cell processes are they involved?

Which two protein families do most actin-binding proteins belong to?

Which protein complex nucleates microtubules in vivo and where does it occur in this capacity?

Which protein is the main component of a basal body

Name 4 types of cell contacts that have a connection to the cytoskeleton and which of the 3 cytoskeletal filament types they are primarily connected to?

For the epithelial cell shown schematically below, draw the position of the 5 different forms of cell contacts and indicate which cytoskeletal system they are connected to (GJ/MT (MT not required), TJ/Akt, Desm/IF, Hemidesm/IF, AdhJ/Akt).

Which 2 fundamentally distinguishable types of adhesive interactions between cells do you know? For each of the two categories, name a cell adhesion molecule for which this type of interaction is the normal case.

Apart from their involvement in cell adhesion, what do the JAM and CAM proteins have in common?

Which two types of filament are found in the cell nucleus?

Which 2 forms of cell contacts mediated by integrins do you know that can be distinguished in terms of interaction with cytoskeletal elements and with which cytoskeletal filament system do they interact in each case?

Name one similarity and one fundamental difference with regard to the proteins involved in hemidesmosomes and desmosomes.

Name one similarity and one fundamental difference with regard to the proteins involved in hemidesmosomes and focal contacts.

Name one similarity and one fundamental difference with regard to the proteins involved in desmosomes and adherens junctions

What are the names of the proteins that primarily mediate cell contact between epithelial cells and between cells and ECM components in the 6 different forms of cell contact discussed in the VL?

Name 3 essential components of the basal lamina

Which cellular membrane protein does fibronectin interact with?

Which substances (at least 3 mentions) can pass through gap junctions and what is their maximum size?

How are gap junctions regulated?

Which characteristic post-translational modification is found in collagen?

Where does the assembly of collagen fibers take place?

To which molecular group does the molecule to which the proteoglycan side chains of an aggrecan aggregate are bound belong?

Name three structural components of the extracellular matrix (exact names)

Which two membrane proteins mediate the initial contact between leukocytes and endothelial cells during diapedesis and thus ensure that the cells are not washed away in the bloodstream but roll slowly along the epithelium?

Which cell adhesion proteins are regulated by calcium?

In which cell connections do these proteins occur?

Name two different types of cell adhesion proteins that are regulated by calcium.

In which cell compounds do these proteins occur?

Do cadherins show their adhesive properties at high or low calcium concentrations?

Name 4 different processes that are regulated by small GTPases.

In which state are small GTPases activated or inactivated and name one type of protein that causes each state.

Give two examples of modular protein structure

Identify 2 important physical/chemical parameters that can differ greatly in different cell compartments

Name the classes of molecules that make up the 4 basic molecular building blocks of the cell

Nennen Sie die Zellzyklusphasen in der richtigen Abfolge (mit welcher Phase Sie beginnen ist egal)

Which enzymes are the most important regulators of the cell cycle?

Which process inactivates a cyclin-dependent kinase (CDK)?

Explain the origin of the name Dynaktin.

Which two main structural components characterize

characterize a centrosome in animals?

a) Which stage of cell division is inhibited by

treatment of cells with nocodazole or colchicine and

b) exactly which process is inhibited by

inhibited by the toxin?

Which dominant cytoskeletal elements and which corresponding motor protein can you find in cilia?

Why do glycans bind so much water and form gels?

gels?

Name a cell adhesion protein anchored in the plasma membrane of cell adhesion protein anchored in the plasma membrane of endothelial cells that prevents contact with leukocytes in the blood during diapedesis

Name three membrane protein components of Tight junctions

You are looking at the amino acid sequence of two

membrane proteins with the following sequence scheme:

a)

xxxxxxxxxxxxx+hhhhhhhhhhhhhhhhhhhhhhhhxxxxxxxxxxxxxxx

xxxxxxxxxxxxxxxx

b)

xxxxxxxxxxxxxhhhhhhhhhhhhhhhhhhhhhhh+xxxxxxxxxxxxxxx

xxxxxxxxxxxxxxxx

(x = any amino acid, + = basic amino acid, h = hydrophobic amino acid).

hydrophobic amino acid). What type of

type of membrane protein is (a) or (b)?

Name 3 forms of non-covalent binding that can take place can take place between protein chains

Which 3 classes of membrane lipids do you know?

Name three essential proteins that are involved in the involved in the pinching off of vesicles during receptor-mediated endocytosis.

What is the function of GTP cleavage by Sar1 or ARF1 after the strangulation of a transport vesicle?

To which structures (type of molecule) do lectins such as calnexin or calreticulin bind to?

How does beta-tubulin at the plus and minus ends of a microtubule differ minus ends of a microtubule with regard to the hydrolysis state of GTP?

What is the basic building block of the a) actin or b)

tubulin filament?

Which molecular complex is required to bind dynein to the to the transported material?

a) Which protein complex nucleates microtubules in vivo and b) where does it occur in this capacity?

a) Which stage of cell division is disturbed by treatment of cells with cytochalasin and b) exactly which process is inhibited by the toxin inhibited by the toxin?

Name 5 mitotic phases in the correct chronological order