Altklausur

Question 1

In E.coli the co translational targeting depends on specific ribonucleoprotein complexes like
- SRP
- SecA
- SecB

Answer 1

SRP

Question 2

The TAT-pathway
- allows the transmembrane transport of folded proteins
- allows the transport of protein complexes already loaded with cofactors
- is also present in plastids

Answer 2

• allows the transmembrane transport of folded proteins
• is also present in plastids

Question 3

In E.coli the topogenesis of membrane proteins of the inner (plasma) membrane occurs in most cases
- co translational
- SecY-dependent
- YidC dependent but not SecY dependent

Answer 3

• co translational

Question 4

Secretion of proteins via the Type IV system (T4SS) requires the hydrolysis of ATP in the
- cytoplasm
- periplasm
- the extracellular space

Answer 4

• cytoplasm

Question 5

The formation of disulphide bounds in secretory proteins occurs in E. coli
- in the cytoplasm
- in the periplasm
- at the extraperiplasmic surface of the outer membrane

Answer 5

• periplasm

Question 6

The lipidation of outer membrane proteins in bacteria occurs
- in the cytoplasm
- at the periplasmic surface of the plasma membrane
- at the periplasmic surface of the outer membrane

Answer 6

• in the cytoplasm

Question 7

The import of proteins into the matrix of mitochondria requires a targeting signal
- that can form a amphipathic helix
- that contains positive charges
- that is enriched in leucines and isoleucines
The process uses
- GTP
- ATP
- PMF
as energy source.

Answer 7

• that can form a amphipathic helix
• ATP

Question 8

beta-barrel proteins (e.g. porins) of the outer mitochondrial membranes are inserted
- directly from the cytoplasm
- using a pathway that crosses the inter membrane space
- using PMF as energy source

Answer 8

• using a pathway that crosses the inter membrane space

Question 9

The inter membrane space
- has a redox potential that supports the formation of disulfide bounds
- has a redox potential that blocks the enzymatic reshuffling of disulfide bounds / requires enzymatic factors for the formation of disulfide bounds
- requires enzymatic factors for the formation of disulfide bounds

Answer 9

• has a redox potential that supports the formation of disulfide bounds

Question 9

The inter membrane space
- has a redox potential that supports the formation of disulfide bounds
- has a redox potential that blocks the enzymatic reshuffling of disulfide bounds / requires enzymatic factors for the formation of disulfide bounds
- requires enzymatic factors for the formation of disulfide bounds

Question 10

Complex plastids
- contain more than two internal membranes
- contain always two genomes of different evolutionary origin
- descend from eukaryotic plastid-containing protists

Answer 10

• contain more than two internal membranes

Question 11

The vesicular transport between the ER and the Golgi apparatus requires the direct involvement of
- a COPII coat
- a COPI coat
- SNAREs

Answer 11

• COPI
• SNAREs

Question 12

The KDEL-receptor usually transports
- soluble proteins from the ER to the Golgi
- membrane proteins from the ER to the Golgi
- Membrane proteins from the Golgi to the ER
if they have the KDEL motif at their C-terminus.

Answer 12

• membrane proteins from the Golgi to the ER

Question 13

The import of activated sugars into the medial Golgi requires
- flippases and isoprenes
- antiporters
- aquaporins

Answer 13

• antiporters

Question 14

The typical stack structure of the Mammalian Golgi is stabilized
- by a static matrix similar to the nuclear lattice
- through interactions between tethering factors which are also involved in membrane traffic through the Golgi and their regulators
- by membrane contact sites which also serve the lipid exchange between Golgi stacks

Answer 14

• through interactions between tethering factors which are also involved in membrane traffic through the Golgi and their regulators

Question 15

The activation of preproproteinconvertases is triggered
- by cholesterol
- by the concentration of calcium ions
- by the pH

Answer 15

• by the concentration of calcium ions

Question 16

Name the two currently discussed mechanisms explaining the formation of secretory storage vesicles

Answer 16

• cleavage by PC3 end-protease and PC2 end-protease
• cleavage by Carboxypeptidase

-> Disulfide bonds hold the rest together so that just A and B segment are left

Secretory vesicles form from the trans Golgi network, and they release their contents to the cell exterior by exocytosis in response to extracellular signals. The secreted product can be either a small molecule (such as histamine) or a protein (such as a hormone or digestive enzyme).

Question 17

Presently there are three pathways discussed describing the behavior of synaptic vesicles. What are the typical properties that are under dispute for the respective pathway in brief?

Answer 17

KISS AND RUN
1) Docking
2) Priming
3) Fusion pore opening
4) Endocytosis
5) NT uptake

KISS AND STAY
1) NT uptake
2) Priming
3) Fusion pore opening

ENDOSOME RECYCLING MODEL
exocytosis/endocytosis cycle with a complete collapse of the vesicle with its target membrane

Question 18

Phagocytosis depends on the reorganization of
- the cortical actin network
- the tubular spindles
- the Golgi apparatus

Answer 18

• the cortical actin network

Question 19

The compartment specific release of ligands from their receptor in the different end-lysosomal compartment is usually regulated by
- the Zn concentration in the compartment
- the luminal pH of the compartment
- the binding of Ram proteins to the luminal domains of the receptor

Answer 19

• the binding of Ram proteins to the luminal domains of the receptor

Question 20

The targeting signal of many enzymes to the lysosome in mammalian cells is
- mannose-6-phosphate
- glucose-1-phosphate
- the SKL-peptide

Answer 20

• mannose-6-phosphate

Question 21

The degradation of lipid vesicles in lysosomes requires the destabilizing activity of
- glycosylated LAMPs
- the lipid LBPA
- activators presenting membrane lipids to lipases

Answer 21

• the lipid LBPA

Question 22

A common feature of cytotoxic T-cells and mast cells is the existence of
- secretory lysosomes
- apical early endoscopes
- melanosomes

Answer 22

• secretory lysosomes

Question 23

Downregulation of membrane receptors (e.g. EGF-receptor) requires
- ubiquitination of cytoplasmic receptor domains
- clathrine-dependent sorting to late endosomes
- ECRT-dependent sorting to internal vesicles of MVB

Answer 23

• ECRT dependent sorting to internal vesicles of MVB

Question 24

Macroautophagy requires the involvement of - ubiqutin-like protein tags - membrane patches of the plasma membrane - membrane patches of the inner nuclear membrane

Answer 24

- ubiquitin like protein tags

Question 25

An important difference between microautophagy in comparison to macroautophagy is - the lack of the formation of a double-membrane structure (phagophore) - the involvement of lysosomal hydrolyses during digestion of the material - the maximal size of objects that can be degraded by this process

Answer 25

- the lack of the formation of a double-membrane structure (Phagophore)

Question 26

Describe briefly (one note for each!) the three currently discussed models, how exocytosis of secretory vesicles or secretory lysosomes may contribute to the repair of small holes on the plasma membrane or membrane ruptures.

Answer 26

SECRETORY LYSOSOMES / MVB - hematopoietic cells (diverse content including exosomes and their content, acid hydrolyses and other proteins) - acrosomes of sperm cells (procathepsin L; but also other models of its origin!) - melanosomes (but also other models) - secretion of morphogens in Drosophila? EXOCYTOSIS OF CONVENTIONAL LYSOSOMES - membrane repair (e.g. fibroblasts, muscle, stomach ...) - "defecation" mechanism by lysosomes in all cells? - secretion is in both cases Ca2+-regulated - machinery for exocytosis includes general but probably also cell-type specific factors

Question 27

Name three pathways for lipid exchange between cellular compartments

Answer 27

- spontaneous exchange only fast for short or single-chain lipids (e.g. minutes for lysophosphatidylcholin) - lipid transport using the membranous transport containers involved in protein transport - lipid transfer proteins; also important for formation of lipid droplets -> a) via Diffusion -> b) via membrane contact sites - lipid exchange between leaflets of the same membrane occurs usually via flippases (ATP-dependent and ATP-independent)

Question 28

Name the main steps during formation of the nucleus after mitosis of a typical mammalian cell

Answer 28

- Dephgosphorylation of components like INM, nuclear pore and lamin - targeting of nucleocytoskeletal proteins and pre-pore forming nucleoporins to the chromosomal surface - chromosome clustering removes cytoplasm from reassembling nucleus - membrane recruitment (reticular ER and/or vesicles) and fusion by interaction of integral membrane proteins of the inner nuclear membrane (INM) with chromatin - formation of ER sheets by enhanced recruitment of integral inner membrane proteins of the INM and of other sheet-forming components into these areas - sealing of the envelop (annular fusion) by p97 and ESCRTIII at those sites, were MT (from the spindle) cross the nucleoplasm - cytoplasm borderline - (final?) assembling of nuclear core complex - transport of the bulk of laming into the nucleus via NPCs - formation of the new lamina

Question 29

The maturation of spliceosomal RNAs involves - a transient presence of several RNA types in the cytoplasm - base modifications for several RNA types in the Canal bodies - base modifications for one type of RNA in the nucleolus

Answer 29

(- a transient presence of several RNA types in the cytoplasm) - base modifications for one type of RNA in the nucleolus

Question 30

Polyadenylation of RNA - is a destabilizing motif in the bacteria - is an enzymatic reaction in eukaryotes inly found during maturation of mRNAs - is a prerequisite for export of most mRNAs from the nucleus

Answer 30

- is an enzymatic reaction in eukaryotes only found during maturation of mRNAs

Question 31

Stress granules - are cytoplasmic membrane surrounded organelles - are storage sites for mRNA, ribosomal subunits and others during stress - are sites of maturation of large ribosomal subunits

Answer 31

- are storage sites for mRNA, ribosomal subunits and others during stress

Question 32

The nonsense-mediated decay (NMD) is a quality control step degrading compromised - small ribosomal subunits - tRNA - mRNA

Answer 32

- mRNA

Question 33

During post-translational transport across the plasma membrane of bacteria SecA - directly recognizes and proof-reads the signal sequence - moves the polypeptide through the SecYEG channel - cleaves off the signal sequence. Sec A needs for this - ATP - GTP - PMF

Answer 33

- moves the polypeptide through the SecYEG-channel - ATP

Question 34

Combine the transporters with their correct function: - Type V autotransporter - Type III secretion system - Tat-transporter - Type I secretory system - Needs SecYEG for the transport step across the plasma membrane - can translocate substrates already folded in cytoplasm - has an ATPase subunit located in the cytoplasm

Answer 34

- Type V autotransporter: needs SecYEG for the transport step across the plasma membrane - Type III secretion system: has an ATPase subunit located in the cytoplasm - Tat transporter: can translocate substrates already folded in the cytoplasm - Type I secretory system: Needs SecYEG for the transport step across the plasma membrane?

Question 35

In proteobacteria the linkage of disulphide bridges occurs usually (in the extracellular space / in the periplasmic space / in the cytoplasm). Finally, the excessive electrons are (usually / depending on the environmental conditions / never) transferred to oxygen. Eubacterial proteins are (often / rarely / never) modified via N-linked glycosylation. Proteins of the periplasm, which do not fold correctly, are usually (degraded by Clp-type proteases after backtranslocation into the cytoplasm / degraded by proteases in the periplasm / disposed by secretion across the outer membrane). The transport of lipids from the plasmamembrane (PM) to the outer membrane (OM) occurs (via vesicles / via Iipid transfer proteins, forming a street-like connection between the PM and the OM , via diffusion of soluble lipid-binding molecules across the periplasmic space).

Answer 35

1. periplasmic space 2. ? 3. often 4. degraded by proteases in the peri plasm 5. via Lipid Transfer Proteins, forming a street like connection between the PM and the OM

Question 36

(The Oxal protein of the inner membrane / protein complexes of the inter membrane space / the ToM-complex) is directly involved in the topogenesis of ß- barrel proteins of mitochondria. Compared to the matrix, the inter membrane space of mitochondria is (oxidising / reducing / slightly acidic). The majority of proteins found in the stroma of plastids that are coded in the nucleus (are imported via the TOC / are imported via the TIC / contain a cleavable transit peptide)). Proteins with an N-linked glycosylation (have so far no been found in plastids I are frequently found with low abundance, due to the weak activity of an oligosaccharyltransferase in the thylakoid membrane / can be found in some rare cases indicating the existence of an import partway which goes across the endoplasmic reticulum). According to the presently best-supported model (are all peroxisomal membrane proteins always imported directly from the cytoplasm into the peroxisome / are some membrane proteins able to enter the peroxisome via the endoplasmic reticulum / are all membrane proteins always entering the peroxisome via the endoplasmic reticulum).

Answer 36

1. The Tom-complex 2. reducing 3. are imported via the TOC / are imported via the TIC 4. can be found in some rare cases indicating the existence of an import pathway which goes across the endoplasmatic reticulum 5. are some membrane proteins able to enter the peroxisome via the endoplasmic reticulum

Question 37

Describe the transport cycte of the KDEL-receptor using the following terms: ER, Golgi, COPI, COPll, pH, cargo-binding, cargo'release, vesicle. Start with the ER

Answer 37

MAINTENANCE OF ER PROTEIN COMPOSITION Two systems: Retention of proteins, retrieval of proteins RETENTION - due to direct or indirect association with cytoplasmic or nucleoplasmic elements (ribosomes, lamins etc) disfavoring entry into exit sites; indirect association could be driven by Ca2+ dependent interactions -due to TMD with weak hydrophobicity RETRIEVAL - NEEDS SORTING SIGNALS - KDELcooh for luminal proteins (recognized by KDEL-receptor family) - others (recognized by Erv41/46) - signal in TM of proteins (recognized by Rer1) - KKXXcooh for membrane proteins and - XXRR- for Type II membrane proteins (both recognized directly by COPI-coat)

Question 38

Secretory granules (SG) are formed at the (TGN / the sorting endosome / the endoplasmic reticulum) and regularly contain enzymes for (processing of pro- peptides / O-glycosylation / disulphide-bound reshuffling). NSF (is an ATPase, which dissolved SNARE bundles / is a v-SNARE / is acting after the fusion pore has formed). Essential factors for clathrine-mediated endocytosis are (Dynamins / SNARE- proteins I AP2l. During micropinocytosis the membrane carriers (may be coated by clathrin / may be coated by calvin I may be without any detectable coat)'

Answer 38

1. TGN = trans Golgi network 2. O-glycosylation? 3. is an ATPase, which dissolves SNARE bundles 4. Dynamins 5. may be coated by Clathrin

Question 39

Explain the term "compensatory endocytosis"

Answer 39

- Endocytosis counterbalances exocytosis (compensatory endocytosis) recycling specific molecules (e.g. SNAREs) or large membrane areas ("excess retrieval"). It regulates the size of the PM and the cell shape. - Endocytosis regulates the capacity of the PM for transport of molecules. - Endocytosis regulates the capacity of the PM for transport of information (receptor down-regulation) -> Endocytosis provides a platform for the integration of cellular signaling pathways -> Endocyosis is involved in cell differentiation and embryonic development via clearance of receptors and joining structures from the PM - Pathogens and toxins usually enter the cell via endocytosis

Question 40

The mannose-G-phosphatereceptor (transports acid hydrolases to the late endosome/lysosome / transports some soluble substrates destined for degradations from the extracellular space towards the late endosome/lysosome / guides defective channels from the plasmamembrane to the late endosome/lysosome). Autophagy is upregulated (during starvation / in order to degrade intracellular pathogenes / during oocyte maturation in mammalia). The membrane of inner vesicles of MVB are enriched in (Cardiolipine I Bis(monoacylglycero)phosphate / Ganglioside). (Lysosoms / secretory granules / early (sorting) endosomes) provide the material for the formation and maturation of melanosomes.

Answer 40

1. transports acid hydrolyses to the late endoscome lysosome 2. during starvation / in order to degrade intracellular pathogens 3. Cardiolipine 4. Lysosomes

Question 41

Name the two main mechanistic causes for the asymmetric distribution of membrane lipids at the eukaryotic plasma membrane

Answer 41

- Glycerophospholipids - Sphingolipids + cholesterol -> lipid micro domains - Bulk synthesis of lipids in the ER, Espresso. also at ER-Mito contact sites - Mito synthesizes 45 % of its lipid content

Question 42

Cytokinesis in mammalian cells, Kormophyten and baker's yeast

Answer 42

- starts usually with the formation of an ingression furrow -> in somatic mammalian cells - requires a break-down of the nuclear envelope - in somatic mammalian cells - needs vesicle transport along microtubules to the mid-lane -> in somatic cells of a Kormophyte - is always morphologically asymmetric -> in cells of Saccharomyces cerevisiae (Baker's yeast) (in somatic mammalian cells) - ends with a structure termed midbody -> Metazoa (Mammalian)

Question 43

For the division of chloroplast the involvement of (2 I 3 / 4) different classes of GTPases are needed. The inheritance of yeast vacuoles requires (a recruitment of ribosomes to the limiting membrane /a fragmentation of the vacuole / a complete block of the metabolic activity of the vacuole). The fusion of somatic mammalian cells (can be observed in vivo / requires SNARE homologs as fusogenes / requires mitofusin homologs as fusogenes). Contact sites between endoplasmic reticulum and mitochondria (are sites of lipid transport between ER and mitochondria / provide channels for the exchange of proteins between the ER lumen and the inter membrane space of mitochondria / define the sites of mitochondrial fission).

Answer 43

1. 2 2. a fragmentation of the vacuole 3. can be observed in vivo 4. define the sites of mitochondrial fission

Question 44

The polyadenylation of a mRNA (is in the cytoplasm of eukaryotic cells always a stabilizing element / is in the nucleus in most cases a stabilising etement / is in the cytoplasm of prokaryotic cells a destabilizing element) The identification of a so-called premature stop codon in mammalian cells (occurs in the nucleus / is only important for the cett in the case of selenium depletion / activates an mRNA-editing machinery to repair the defective codon). Stress granules (are membranous organelles, which form in the cytoplasm / are sites for storage of ribosomes, mRNAs and preinitiation complexes / may exchange their materia! with so-called processing bodies). The nascent chains of stalled ribosomes in cytoplasm yeast (are degraded via the proteasome / are covalently linked to the mRNA tagging the molecute for degradation / can be deposited in aggregates).

Answer 44

1. is in the cytoplasm a prokaryotic cells a destabilizing element 2. occurs in the nucleus? -> activates decay 3. are sites for storage of ribosomes, mRNAs and preinitiation complexes 4. are degraded via the proteasome

Question 45

Link the statements (1 to 12) to the viruses (A and B) by writing the statement numbers behind the correct virus. Multiple links are possible (incorrect answers cost points) 1. 2-,3- and S-fold symmetry 2. A hypodermic "nano"-syringe 3. Helicalsymmetry 4. 12 faces, each with a S-fold symmetry 5. 12 vertices, each with a S-fold symmetry 6. g8p major coat protein, 2700-3000 copies 7. \=4 8. Amplitude and pitch 9. Jelly roll structures 10. P=µxp 1 1. Chymotrypsin-like fold 12. Canyon binder drugs A. Phage M13: B. Picornaviruses:

Answer 45

PHAGE M13 - P = µ x p - helical symmetry - g8p major coat protein, 2700 - 3000 copies PICORNAVIRUSES - Jelly roll structures

Question 46

a) The lnfluenza HA surface glycoprotein is a lectin. b) HA auto-catalytically cleaves itself into two fragments, HAI and HA2. c) The first 20 amino acids of the N-terminus of HA2 constitute the so-called fusoqenic peptide. d) HA binds sialic acid residues of host-glycoproteins. e) At high pH a substructure of HA rearranges into a 6-helix-bundle. 0 Fusion inhibitors affect HA 6-helix-bundle formation, which is mandatory for infectivity.

Answer 46

a) WRONG b) WRONG c) RIGHT d) RIGHT e) ? f) RIGHT

Question 47

Different statements regarding: - Tat, transactivator of transcription - lntegrase - REV, regulator of expression of virion proteins - Vif, viral infectivity factor - Vpu, viral protein out Vpr, viral protein rapid - Nef, non-evident function Proteinase - Reverse transcriptase - GP41 - GP1 20 - CA, capsid protein

Answer 47

- Vif- viral infectivity factor: Hijacks the cellular Cullin5 E3 ubiquitin ligase to ubiquitinylate APOBEC3G - REV, regulator of expression of vision proteins: lnvolved in splicing and nuclear export of viralmRNA - RNA-RNA duplex dependent RNase activity - Tat, transactivator of transcription: Activates CDKg by binding to Cyclin T1 of elonqation factor P-TEFb - Vpu, viral protein out: lnduces ubiquitinylation and deqradation of CD4 - CA, capsid protein: Penta- and hexamer tyPe Protomers - Vpr, viral protein rapid: G2 cell cycle arrest to endorse viral LTR activity - RNA-dependent RNA polymerase: Reverse transcriptase - Nef, non evident function: MHC-class-1 and -2 antiqen reduction

Question 47

Different statements regarding: - Tat, transactivator of transcription - lntegrase - REV, regulator of expression of virion proteins - Vif, viral infectivity factor - Vpu, viral protein out Vpr, viral protein rapid - Nef, non-evident function Proteinase - Reverse transcriptase - GP41 - GP1 20 - CA, capsid protein

Answer 47

- Vif- viral infectivity factor: Hijacks the cellular Cullin5 E3 ubiquitin ligase to ubiquitinylate APOBEC3G - REV, regulator of expression of vision proteins: lnvolved in splicing and nuclear export of viralmRNA - RNA-RNA duplex dependent RNase activity - Tat, transactivator of transcription: Activates CDKg by binding to Cyclin T1 of elonqation factor P-TEFb - Vpu, viral protein out: lnduces ubiquitinylation and deqradation of CD4 - CA, capsid protein: Penta- and hexamer tyPe Protomers - Vpr, viral protein rapid: G2 cell cycle arrest to endorse viral LTR activity - RNA-dependent RNA polymerase: Reverse transcriptase - Nef, non evident function: MHC-class-1 and -2 antiqen reduction

Question 48

Different statements regarding: - Tat, transactivator of transcription - lntegrase - REV, regulator of expression of virion proteins - Vif, viral infectivity factor - Vpu, viral protein out Vpr, viral protein rapid - Nef, non-evident function Proteinase - Reverse transcriptase - GP41 - GP1 20 - CA, capsid protein

Answer 48

- Vif- viral infectivity factor: Hijacks the cellular Cullin5 E3 ubiquitin ligase to ubiquitinylate APOBEC3G - REV, regulator of expression of vision proteins: lnvolved in splicing and nuclear export of viralmRNA - RNA-RNA duplex dependent RNase activity - Tat, transactivator of transcription: Activates CDKg by binding to Cyclin T1 of elonqation factor P-TEFb - Vpu, viral protein out: lnduces ubiquitinylation and deqradation of CD4 - CA, capsid protein: Penta- and hexamer tyPe Protomers - Vpr, viral protein rapid: G2 cell cycle arrest to endorse viral LTR activity - RNA-dependent RNA polymerase: Reverse transcriptase - Nef, non evident function: MHC-class-1 and -2 antiqen reduction

Question 49

Describe the pathway used by SV40 to its site of genome replication

Answer 49

1. Endocytosis into Calveolae 2. Fusion with Caveosome, no pH shift 3. Long transport in vesicles; actin, Rho-GTPase and microtubule-dependent into the ER 4. Structural rearrangement of the capsid in the reducing milieu of the ER, mysristylated N-term of VP2 exposed 5. Penetration into cytoplasm; ERAD pathway! (ER-associated protein degradation complex) 6. Import into nucleus by NPC and NLS in VP2/3

Question 50

At which intracellular membrane system does the RNA replication of the following viruses occur?

Answer 50

SARS coronavirus: ER Sindhis virus (Alphavirus): modified Endosomes and lysosomes Flockhouse virus: Outer Mitochondrial Membrane Poliovirus: membrane-coated vesicles

Question 51

Describe the properties of RIG I

Answer 51

-C-terminal regulatory domain - 5' PPP RNA (also when ss) - short blunt ds region (also without 5' PPP) e.g. panhandle of ss (-) RNA virus - poly Uridine stretches

Question 52

At which step does Influenza virus interfere with the RIG I signaling pathway? Which viral protein is required for interference

Answer 52

Influenza A virus nonstructural protein 1 (NS1) specifically inhibits TRIM25-mediated RIG-I CARD ubiquitination, thereby suppressing RIG-I signal transduction.

Question 53

Virus evolution. What is a "bottle neck" experiment? Explain briefly by describing an example

Answer 53

- Selection: e.g. by neutralizing monoclonal antibodies or antivirals in cell culture supernatants - massive reduction of heterogeneity in population

Question 54

The infection of members of the genus Flavivirus involves the process of membrane fusion. What is the role of prM during maturation of the visions of these viruses? Describe this process and the role of prM.

Answer 54

prM: protection form fusion during budding; Turin cleaves prM into pr and M (in TGN) 1) Co translational association with helper protein (e.g. prM in Flavi-, E2 for Alphaviruses) 2) Helper protein blocks fusion activity; protects virus from premature fusion 3) proteolytic cleavage of helper proteins is a requirement for fusion activity of the fusion protein 4) Due to a low pH in the secretory pathway, pr peptide remains bound to E even after proteolysis and still protects virus from premature fusion with the host cell membrane 5) After secretion into the extracellular milieu (neutral pH), pr peptide is released and the fusion loop in E (internal loop not terminal like class I fusion peptide) becomes fusion active 6) At neutral pH E is a dimer lying flat on the vision; at low pH in the end-some E is converted into a conformation protruding from the vision surface which allows insertion of the fusion loop onto the Endosomal membrane 7) this triggers trimerisation of E which triggers the conformational change leading to the approach of membranes and their fusion

Question 55

How are retroviruses traveling directly from cell to cell? Describe briefly the mechanism and the functional role of the cell associated retroviral ENV protein in this process?

Answer 55

ENV: promotes export of mRNA out of the nucleus spread cell-to-cell by induction of multimolecular complexes termed virological synapses that assemble at the interface between infected and receptor-expressing target cells.

Question 56

Describe the domain structure of the protein "p" of Hepatitis B virus in a scheme.

Answer 56

- inckudes motifs in Pol/RT and RH which are shared with retroviral RT Additional domain: TP (terminal protein)-domain without know homolog

Question 57

Before "p" can start the cDNA synthesis on the viral RNA an activation step is required. Describe this activation step and explain the priming reaction in detail. Name the involved molecules and explain the individual steps with a scheme.

Answer 57

All DNA-polymerases need a "primer" (3'-OH end) for initiation of DNA synthesis - 5' base of (-)-DNA covalently bound to tyrosine in TP-domain of P > "protein priming" - P protein accepts no other template RNA than pgRNA (<>cDNA synthesis!= - 5' end of (-)-DNA localizes in 3' proximal DR1 (direct repeat 1) - UUC sequence in DR1 exists also in the epsilon bulge region (sequence of duck HBV) - Its complementary sequence AAG in the (-)-DNA represents a copy thereof - epsilon contains origin of replication for (-) DNA - (-) DNA Synthesis is discontinuous -> Retroviruses are similar in their mechanisms

Question 58

The cellular m:R-l22 is a critical host factor for the Hepatitis C Virus life

Answer 58

- miR-122 stimulates HCV RNA synthesis prior to promoting viral protein synthesis by displacing PCBP2 from the viral RNA genome via competition with PCBP2 for binding to the 5' UTR. This mode of action promotes an open, noncircular genome conformation

Question 59

Proteins using the GEP (general excretion pathway) may be translocated (while being synthesized (cotranslationally) / after termination of their synthesis / before termination of transcription of the corresponding gene).

Answer 59

- while being synthesized (cotransaltionally)

Question 60

The GEP is the only pathway that (transports soluble proteins into the periplasm / that integrates membrane proteins into the plasma membrane / that integrates porins into the plasma membrane).

Answer 60

- that integrates membrane proteins into the plasma membrane

Question 61

In some pathways, the GEP-dependent transport is regulated by (a GTPase / a system of two GTPases / is only regulates by ATPases).

Answer 61

- is only regulated by ATPases

Question 62

The GEP is usually able to transport (unfolded proteins / folded proteins / tRNAs).

Answer 62

- folded proteins

Question 63

The periplasmic space of E. coli (is reducing and thus allows the formation of disulfide bridges / is ATP-rich and thus allows the folding of proteins / is free of soluble proteases, therefore misfolded soluble proteins need to be reimported into the cytoplasm for degradation).

Answer 63

- is free of soluble proteases, therefore misfiled soluble proteins need to be reimported into the cytoplasm for degradation

Question 64

For the maintenance of the outer membrane of E. coli (proteins with ß-barrel folds must be integrated / lipopolysaccharides must be translocated to the outer leaflet / cholesterol is translocated across the periplasm).

Answer 64

- lipopolysaccharides must be translocated to the outer leaflet

Question 65

The translocation of nuclear-coded proteins into the matrix of mitochondria occurs with the direct involvement of (the TOM-complex / the TIM22-complex / mtHSP70).

Answer 65

- the TOM-complex - the TIM22-complex

Question 66

TIM 9/10 is a complex of the intermembrane space, which is essential for the (integration of carrier proteins into the inner membrane / the translocation of proteins into the matrix / the biogenesis of ß-barrel proteins of the outer membrane) whos activity depends on the presence of (ATP / GTP / CTP).

Answer 66

- Integration of carrier proteins into the inner membrane? - ATP

Question 67

Proteins of the matrix that do not fold properly are usually degraded (in the matrix / in the intermembrane space / in the cytoplasm).

Answer 67

- in the cytoplasm

Question 68

Name the two ways discussed for the formation of Secretory granules (dense core vesicles).

Answer 68

- Condensing vacuole model - homotypic fusion model

Question 69

Describe the major differences between „fluid-phase endocytosis“ and “receptor-mediated endocytosis“. Would the term „Pinocytosis“ match to any of these processes, and if so, why?

Answer 69

- low efficiency, non specific - nonspecific mammalian cells drink about one volume per day - nutrients may be concentrated in lysosomes by uncharacterized mechanisms -> can be summarized as Pinocytosis "senso stricto" Receptor mediated endocytosis: uptake of up to 30 % of bound ligands per minute

Question 70

„Multivesicular bodies“ (MVB) can be part (of a degradation pathway / of a secretion pathway). They contain internal vesicles, into which (membrane proteins / soluble proteins) are sorted, which usually have been tagged before by a (monoubiquitination / sumoylation / polyubiquitination).

Answer 70

- of a secretion pathway - membrane proteins - ?

Question 71

The following parts of a cell can be selectively targeted by autophagy (peroxisomes / mitochondrial ribosomes / midbodies). During formation of the autophagosome in macroautophagy lipids in the phagophore are (modified via O-glycosylation / modified via ubiquitination / enriched in sphingomyelin). In chaperone-mediated autophagy (only small organelles are digested / chaperones located in the lysosomal lumen are involved / cytoplasmic ATPases are involved).

Answer 71

- peroxisomes, ribosomes, - modified via ubiquitination - chaperones located in the lysosomal lumen are involved

Question 72

Name three fundamental mechanisms that are responsible for the asymmetric distribution of lipids between the leaflets of the plasma membrane

Answer 72

Most of the Phosphatidylserine (PS) is located on the cytosolic site of the plasma membrane - Generation and maintenance of PS asymmetry by an energy-dependent flip-awe (ATP hydrolysis)

Question 73

Which are the two main pathways for delivery of lipids from the ER to the TGN?

Answer 73

early targeting at Lipid droplet formation sites during formation, and late targeting to mature lipid droplets after their formation

Question 74

During cytokinesis the new plasmamembanes are formed (before disassembling of the actin ring / under involvement of ESCRT-proteins / after division of the midbody into two equal pieces) The source of the additional membrane needed is mainly from (the outer mitochondria membrane | the peroxisome | the outer shell of lipid droplets). During open mitosis, the disassembling of the nuclear membrane requires (the phosphorylation of proteins of the nuclear lamina / the proteolysis of the nuclear pore / the transformation of sheet-like ER into tubular ER). ER-stacks in professional secretory cells like B-cells are only stable in the presence of (tight junctions / neurofilaments / ER-cisGolgi contact sites).

Answer 74

- after division of the middy into two equal pieces - by fusion of vesicles - the transformation of sheet-like ER into tubular ER - ER-cis Golgi contact sites

Question 75

Which function have sno / scaRNA during ribosome biogenesis? Where in the cell do they perform this function precisely? Are members of these RNAs also involved in the biogenesis of other RNPs and if so of which ones?

Answer 75

- guide modification in the nucleoli -> Box C/D snoRNAs guide 2'O methylation -> Box H/ACA snoRNAs guide pseudouridylation

Question 76

Capsid of human rhino virus

Answer 76

- Canyon-binder drugs target VP1 and prevent uncoating of the viral capsid. - 5 copies of VP1 form the so-called "molecular mountains".

Question 77

Bacteriophage MS2

Answer 77

- The capsid triangulation number T equals 3 (T=3). - The icosahedron shell is made up of a single type of coat protomer.

Question 78

Influenza virus Neuranimidase (NA)

Answer 78

- HA is cleaved by the host cell tryptase Clara into two fragments, HA1 and HA2 - The so-called fusogenic peptide, exposed at low/acidic pH, is part of the HA2 fragment. -

Question 79

Link the statements (1 to 12) to the proteins (A to D) by writing the statement numbers behind the proteins/colons. Multiple links are possible. (incorrect links lead to the deduction of points) 1. CCR5 2. RNA polymerase II 3. Proofreading 4. Ubiquitin ligase recruitment to degrade cellular cytidine deaminase 5. Crm1 - Ran.GTP - eIF-5A export pathway 6. Arrest of proliferating cells at G2/M phase 7. CD4 receptor binding to evoke receptor ubiquitination and degradation 8. 6-Helix-bundle formation 9. tRNA(Lys3) 10. Regulator of viral RNA splicing 11. RNAseH Domain 12. Affects the innate defense factor APOBEC3G A GP120 B Reverse Transcriptase C Vif protein D Rev protein

Answer 79

- Vif protein: ubiquitin ligase recruitment to degrade cellular cytidine deaminase - Reverse Transcriptase: tRNA (Lys3), RNAseH Domain - Vif protein: Affects the innate defense factor APOBEC3G

Question 80

At which membrane does the budding of retroviruses occur? - ER membrane - intermediate compartment - Golgi membrane - plasma membrane

Answer 80

- plasma membrane

Question 81

Which cellular pathway and protein complexes are involved in retroviral budding? State the names of the pathway and protein complexes.

Answer 81

D type retrovirus preassembled "Gag" particles

Question 82

Which signals in the viral proteins are recognized by the cellular proteins in this pathway? State the name of the signal and describe it in detail for one viral protein and name for this viral protein its cellular interaction partner.

Answer 82

HA and M2 are required for budding and release - amphipathic helix of M" is sufficient to induce vesicle budding and release - localizes to the point of membrane scission (neck) (immmuno-gold labeling) - virus mutant in M2 helix is impaired in membrane scission -> virus arrays: like beads on a string - M2 is essential for pinch off

Question 83

(+)-strand RNA viruses restructure the intracellular membrane systems of the host cell for their genome replication. Name for each of the compartments listed below one virus which makes use of these membranes for genome replication: - ER - Golgi - Lysosomen - Mitochondrien

Answer 83

ER: Kunjin virus (Flavivirus) Golgi: Kunjin virus (Flavivirus) Lysosomen: Rubella virus Mitochondrien: Flock house virus

Question 84

For viruses restructuring the ER two basic models/mechanisms how the membrane spherules are generated were postulated based on these analyses. Name the two models/mechanisms and give for each one a viral example.

Answer 84

- Virus induced membrane vesicle - replicating RNA reistant to RNAses - NTPs etc must have access - shielding from immune system? ("innate immunity"; interferon)

Question 85

Describe a technical device (apparatus) which allows to study the polarity of virus release from infected cells? Use a scheme. Explain why a certain cell type is required for such a study. Name cell type and its specific features. State one viral example (virus and family) for each of the possible polarities.

Answer 85

Cell culture in a membrane coated chamber; selective release of viruses into the media above or under the cells? Epithelial cells which can be divided into apical (towards the environment) and basolateral (towards the inside of the body) Apical: Paramyxoviridae -> SARS coronavirus Basolateral: Crimean-Congo hemorrhagic fever virus

Question 86

Explain the generation, the function/mode of action of the pr peptide during virion morphogenesis for members of the genus Flavivirus.

Answer 86

- Due to a low pH in the secretory pathway, pr peptide remains bound to E even after proteolysis and still protects virus from premature fusion with the host cell membrane - after secretion into the extracellular milieu (neutral pH), pr peptide is released and the fusion loop in E (internal loop not terminal like class I fusion peptide) becomes fusion active

Question 87

A minority of viruses utilize non-canonical mechanisms in the biogenesis of miRNA molecules. Which of the following answers is/are correct/wrong?

Answer 87

- some viral pre-miRNAs are transcribed by RNA polymerase III - all viral pre-miRNAs are exported into the cytoplasm by exportin-5 - all viral pre-miRNAs are processed by dicer

Question 88

Der SecY-abhängige post-translationale Transport von Proteinen über den General Excretion Pathway (GEP) verwendet als Energiequelle [ ATP | die PMF | GTP ].

Answer 88

- ATP

Question 89

Der GEP ist beteiligt an der [ Sekretion von Proteinen mittels Autotransportern | beim TAT-Transportweg | bei der Biogenese von Typ I Pili ].

Answer 89

- beim Tat-Transportweg

Question 90

Typ III Sekretion benutzt einen makromolekularen Komplex [ der drei Membranen durchqueren kann | der homolog zu Teilen bakterieller Flagellen ist | der ausschließlich co-translational funktioniert ] .

Answer 90

- der drei Membranen durchqueren kann

Question 91

Die Typ I Sekretion verwendet als ATPasen Vertreter der [ ABC-Transporter | der AAA-ATPasen | der F0/F1-ATPasen ] .

Answer 91

- ABC Transporter

Question 92

Der Import von Proteinen in die Matrix der Mitochondrien verwendet eine [ saure | amphipathische | hydrophobe ] Signalstruktur, die in Gegenwart ihres Rezeptors [ eine Helix | eine ß-Faltblattstruktur | ein sogenanntes ß-barrel ] bildet.

Answer 92

- hydrophob -

Question 93

Das Mitochondriengenom der Säuger codiert für [ Proteine der äußeren Mitochondrienmembran | Proteine der inneren Mitochondrienmembran | tRNAs der Matrix ] .

Answer 93

- tRNAs der Matrix

Question 94

Im Zellkern codierte Säugerproteine der inneren Membran, die ein internes Targetingsignal besitzen, nutzen zur Insertion [ den TOM complex | den TIM 22 complex | das mtSecY ] .

Answer 94

- den TIM22 complex

Question 95

Ordnen Sie die nachfolgend genannten Komponenten des Proteintransportes in die Chloroplasten dem Kompartiment zu, in dem sie vorkommen. Geben Sie auch an, in welchem Kompartiment die Abspaltung des Transitpeptides erfolgt. Komponenten: TOC, TIC, cpSecY, cpTAT Äußere Membran Intermembranraum Innere Membran Stroma Thylakoidmembran Das Transitpeptid wird im ........................ abgespalten.

Answer 95

Äußere Membran: TOC Innere Membran: TIC Thylakoidmembran; cpSecY Stroma: cpTAT Das Transitpeptid wird im Strom gespalten.

Question 96

Welche(r) der genannten Mechanismen kommt beim „dual targeting“ tatsächlich vor? [ Ein Molekül einer Population gelangt zu einem Zeitpunkt X entweder in ein Kompartiment A oder in ein Kompartiment B. | Jedes Molekül der Population kommt zumindest teilweise in Kontakt zu Kompartiment A, bevor es entweder in A verbleibt oder nach B umdirigiert wird. | Moleküle gelangen in Abhängigkeit von zellphysiologischen Zuständen eher nach A oder eher nach B ].

Answer 96

Moleküle gelangen in Abhängigkeit von zellphysiologischen Zuständen eher nach A oder eher nach B ].

Question 97

Der COPII-coat ist am Transport vom .............. zum ................ beteiligt. Der KDEL-Rezeptor dient der Rückführung von Proteinen aus dem ........................... zum ................ . Der Import von Zuckern in den Golgi erfolgt mittels [ Isoprenen über Flippasen | Antiportern | Hexose resp. Pentose-Phosphaten als Transportform ]. In Säugerzellen befinden sich die ER-exit sites [ i.d.R. in der Nähe des Golgi- Apparates | über das ER-Netzwerk verteilt | auch an der inneren Kernmembran]. Ein entscheidender Auslöser für die Aktivierung von Preproteinkonvertasen ist der im Verlauf des sekretorischen Weges ........................ pH-Wert im Lumen.

Answer 97

Der COPII coat ist am Transport vom ER zum ERGIC/cis-Golgi beteiligt. Der KDEL-Rezeptor dient der Rückführung von Proteinen aus dem Cis-Golgi zum ER. - antiportern - i.d.R. in der Nähe des Golgi-Apparates Ein entscheidender Auslöser für die Aktivierung von Preproteinkonvertasen ist der im Verlauf des sekretorischen Weges SAURE pH-Wert im Lumen.

Question 98

Synaptische Vesikel der Säuger haben normalerweise einen Durchmesser von [ 2nm | 2 μm | 2mm ] . Die Fusion der Vesikel wird durch den Einstrom von ...............-Ionen getriggert. Tetanusneurotoxin hemmt die Fusion synaptischer Vesikel ............................................... eines SNARE –Proteins. Die Endocytose von Rezeptoren kann [ mittels Clathrine-coats | mittels Caveoline| mittelsCoatamer]erfolgen.

Answer 98

- 2 nm - Calcium-Ionen - SPALTUNG eines SNARE-Proteins - mittels Clathrine-coats

Question 99

Der spezifische Abbau von Lipidvesikeln in Lysosomen wird ermöglicht durch die schützende Wirkung der ...................................... auf die Grenzmembran der Lysosomen und die destabilisierende Wirkung von ................................................... auf die internalisierten Membranvesikel.

Answer 99

- Aktivatoren - Special lipid composition and a low lateral pressure

Question 100

Beschreiben Sie in drei Hauptphasen der Zytokinese bei Säugerzellen

Answer 100

1. Anaphase - Telophase - begin go the assembling of the constriction ring at the PM in the midplane of the cell - ingression of the furrow by the actin-myosin ring till the spindle in the midplane is compressed -> formation of midbody 2. Abscission - disassembling of the contractile ring and the spindle in parallel to the sealing of the PM

Question 101

Kreuzen Sie die richtigen Aussagen an. Im Rahmen der „organellar inheritance“ während der Mitose fusionieren große Teile des Golgi-Apparates mit dem endosomal/lysosomalen Kompartiment. Bei der Teilung der Chloroplasten wird zuerst das Membransystem der Thylakoide, dann die innere Membran und zum Schluss die äußere Membran geteilt. Die homotypische Fusion von Mitochondrien der Säugerzellen erfolgt mittels SNARE-Proteinen.

Answer 101

- Im Rahmen der „organellar inheritance“ während der Mitose fusionieren große Teile des Golgi-Apparates mit dem endosomal/lysosomalen Kompartiment. - Bei der Teilung der Chloroplasten wird zuerst das Membransystem der Thylakoide, dann die innere Membran und zum Schluss die äußere Membran geteilt.

Question 102

Neben rRNA, tRNA und mRNA haben eukaryontische Zellen verschiedene evolutionär konservierte sogenannte „kleine RNAs“. Nennen Sie drei Beispiele hochkonservierter Arten und ihre Funktion in der Zelle

Answer 102

-> miRNA: may regulate the function and stability of target mRNAs by different mechanisms -> piRNA: down regulation of transcripts form transposons thus controlling their spreading in the genome -> endogenous siRNA: can repress gene expression post transcriptionally but have also been shown to affect transcription of specific loci and chromosome structure

Question 103

Die Insertion von Proteinen in die innere Membran von E. coli erfolgt (immer / in der Regel / selten) post translational. Als wichtige Membranproteine können daran (SecYEG / YidC / TRAP) beteiligt sein.

Answer 103

- immer - SecYEG / YidC

Question 104

Der TAT-pathway (kann mit Cofaktoren beladene, gefaltete Enzyme über die innere Membran transportieren / verwendet oft lepB zur Abspaltung des Targetingsignales / wird durch Argenine im N-terminalen Bereich des Targetingsignales blockiert).

Answer 104

- kann mit Cofaktoren beladene, gefaltete Enzyme über die innere Membran transportieren / verwendet oft lepB zur Abspaltung des Targetigsignales

Question 105

Proteine der äußeren Membran von Proteobakterien (sind in der Regel mittels alphahelikalen hydrophoben Abschnitten in der Membran integriert / werden oft vermittels des SecYEG-Komplexes über die innere Membran transportiert / sind – genauso wie die LPS-Moleküle der Membran – immer stark glycosyliert).

Answer 105

- werden oft vermittels des SecYEG-Komplexes über die innere Membran transportiert

Question 106

Proteine der äußeren Membran von Proteobakterien (sind in der Regel mittels alphahelikalen hydrophoben Abschnitten in der Membran integriert / werden oft vermittels des SecYEG-Komplexes über die innere Membran transportiert / sind – genauso wie die LPS-Moleküle der Membran – immer stark glycosyliert).

Answer 106

- werden oft vermittels des SecYEG-Komplexes über die innere Membran transportiert

Question 107

Describe the properties of RIG I

Answer 107

- retinoid acid inducible gene I - Helikase -> intracellular receptor - restriction factor - recognizes RNA viruses like Hepatitis C, Influenza - pattern recognition receptor

Question 108

Which of the following statements about the capsid of tomato bushy stunt virus is/are wrong? Multiple answers are possible. (incorrect answers lead to the deduction of points) (2.5 P) a) The capsid protein has 3 domains (R, S and P) and can adapt to 3 different environments. b) The capsid triangulation number T equals 3 (T=3). c) The P-domains form in total 60 protrusions on the outer surface of the capsid. d) The icosahedron shell displays 12 x 5-fold, 20 x 3-fold and 30 x 2-fold rotation axis. e) The small S domains cover the outside of the capsid and form an external framework. Wrong answers are:

Answer 108

c) The P-domains Form in total 60 protrusions on the outer surface of the capsid. d) The icosahedron shell displays 12 x 5-fold, 20 x 3-fold and 30x2-fold rotation e) The small S domains cover the outside of the capsid and form an external framework.

Question 109

Which of the following statements about the capsid of picornaviruses is/are wrong? Multiple answers are possible. (incorrect answers lead to the deduction of points) a) The capsid contains 60 copies each of proteins VP1 to VP4. b) VP2 and VP3 are located at the top of the so-called molecular mountains. c) VP1 to VP3 form jelly-roll-barrel structures. d) The capsid triangulation number T of picornaviruses equals 4 (T=4). e) Canyon-binder drugs target VP1 and prevent uncoating of the viral capsid. Wrong answers are:

Answer 109

b) VP2 and VP3 are located at the top of the so-called molecular mountains. d) The capsid triangulation number T of picornaviruses equals 4 (T=4).

Question 110

Which statements concerning potential modes of action of viral miRNAs are correct? (cross correct answers; wrong answers will lead to the deduction of points) (2.5 P)  Viral miRNAs can regulate the translation of viral transcripts if the miRNAs are not 100 percent complementary to the viral target mRNAs.  miRNAs of DNA viruses can stimulate the RISC-mediated destruction of viral transcripts if the miRNAs have been transcribed in „antisense“ orientation to the corresponding viral transcript.  miRNAs of DNA viruses can stimulate the RISC-mediated destruction of viral transcripts if the miRNAs have been transcribed in „sense“ orientation to the corresponding viral transcript.  Viral miRNAs can function as orthologs of cellular miRNAs if they share with these cellular miRNAs an identical 6 nucleotides long sequence at the 5‘-end of the miRNA.  Viral miRNAs can function as orthologs of cellular miRNAs if they share with these cellular miRNAs an identical 6 nucleotides long sequence at the 3‘-end of the miRNA.

Answer 110

- Viral mRNAs can regulate the translation of viral transcripts if the miRNAs are not 100 percent complementary to the viral target mRNAs - miRNAs of DNA viruses can stimulate the RISC-mdeiated destruction of viral transcripts if the miRNAs have been transcribed in "antisense" orientation to the corresponding viral transcript.

Question 111

Viruses use different routes for infection. Name for each route one viral example and state whether the virus replicates there or spreads systemically: (wrong answers will lead to the deduction of points) Digestive tract: Eye: Urogential system:

Answer 111

Digestive tract: Local replication -> Corona Eye: Local replication: Adenovirus Urogenital system: Local replication: HPV

Question 112

Viruses have different tissue tropisms. Name one example for each of the following tropisms. (wrong answers will lead to the deduction of points) Epithelotropic: Lymphotropic: Neurotropic: Hepatotropic:

Answer 112

Epithelotropic: Papilloma Virus Lymphotropic: Eppstein Barr Virus Neurotropic: Herpes virus Hepatotropic: Hepatitis Pathogenese HAV, HBV, HCV

Question 113

Name four mechanisms how to bend a membrane

Answer 113

CLUSTERING Transmmebrane proteins with inherent curvature inducing curvature in a membrane MOTIF INSERTION Insertion of a piece of a protein into one leaflet of the membrane induces curvature BAR DOMAINS A BAR domain of a protein inducing and stabilizing the curvature of a membrane SCAFFOLDING - cage like structure of Cathrin - when this structure forms around a membrane, it pulls the membrane into a tight curvature until eventual vesicle budding CYTOSKELETON The inherent shape of a cell as controlled by its cytoskeleton requires that the bilayer membrane curves around it

Question 114

Name four viruses from different families (name virus and family) which can cause hemorrhagic fever

Answer 114

- Flavivirus: Dengue, Yellow Fever - Bunyaviruses: Crimean-Congo hemorrhagic fever virus (CCHFV) - Hantavirus

Question 115

Which ARBO virus was recently introduced into the Americas and is suspected to cause severe brain damage in human fetuses? Name virus, family, genus and vector.

Answer 115

Zika Virus Familie: Flaviviridae Genus: Flavivirus

Question 116

List three cellular sensors of double stranded RNA

Answer 116

- RIG I like receptors - protein kinase R - oligoadenylate synthases - adenosine deaminase

Question 117

What other features of an RNA can be recognized by the innate immune system? Name the features and the relevant sensors for the innate response.

Answer 117

PPPRs = pattern recognition receptors PAMP = pathogen associated molecular pattern

Question 118

How does Influenza virus interfere with signal transduction upstream of IPS1 (=MAVS, CARDIF, VISA)?

Answer 118

Influenza A virus nonstructural protein 1 (NS1) specifically inhibits TRIM25-mediated RIG-I CARD ubiquitinazion, thereby suppressing RIG-I signal transduction.

Question 119

What was the so called “Rabbitpox-Experiment”? What was the outcome and what could be learned?

Answer 119

Release of Myxomatosis-virus to control population of European rabbit introduced by immigrants -> Spread by fleas and mosquitos (passive, no replication in Athropodes) -> 90 - 99 % lethal for European rabbits 1. year: Mortality rate 99,8 % -> Effizienz killing of rabbits 2. year: Mortality rate only 25 % -> Rapid selection of adaptive mutations in the virus (and the host) -> Attenuated virus variants / host population in between only a few years Later years -> Mortality lower than birth rate of rabbits ADAPTION BETWEEN HOST AND VIRUS! (kind of "bottle neck experiment" -> the ones that couldn't cope died)

Question 120

Which of the following statements about the Influenza virus Neuranimidase (NA) and Hemagglutinin (HA) is/are wrong? Multiple answers are possible. (incorrect answers lead to the deduction of points) HA is cleaved by a host cell tryptase (Clara) into two fragments, HA1 and HA2. The so-called fusogenic peptide, exposed at high pH, is part of the HA1 fragment. NA is a muraminidase that can be inhibited by Penicillin. 4 NA molecules, each displaying a 4-bladed propeller, form the functional biological unit. Fusion Inhibitors affect HA 6-helix-bundle formation required for infectivity

Answer 120

- HA is cleaved by a host cell try-taste (Clara) into two fragments, HA1 and HA2. - The so-called fusogenic peptide, exposed at high pH, is part of the HA1 fragment. - NA is a muraminidase that can be inhibited by Penicillin.

Question 121

Link the items (1 to 10) to the viruses (a to c) by writing the item numbers behind the viruses (behind the colons). Multiple links are possible. (incorrect links lead to the deduction of points) 1. Triangulation number T = 3 2. ±16 (16.3) coat proteins per helical turn 3. Jelly roll of 8 ß-strands and a Greek key motif 4. Non-enveloped DNA virus 5. Viral lysozyme required to enter the host cell 6. 3 copies each of VP1 and VP4 arrange around pseudo 6-fold rotation axes 7. 60 copies of VP1 to VP4 8. Total of 12 x 5-fold, 20 x 3-fold and 30 x 2-fold axes 9. Canyon binder drugs 10. A few thousand coat protein copies make up the capsid a) Tobacco mosaic virus: b) Picornavirus: c) Bacteriophage T4:

Answer 121

a) Tobacco mosaic virus: - 16.3 coat proteins per helical turn b) Picornavirus: - 60 copies of VP1 to VP4 - Triangulation number T = 3 - Canyon binder drugs c) Bacteriophage T4: - Triangulation number T = 3

Question 122

Name three viruses with high tissue specificity and three with low tissue specificity: (wrong answers will lead to the deduction of points) High tissue specificity: Low tissue specificity:

Answer 122

High tissue specificity: - Herpesviruses - Papillomaviruses - Retroviruses - Hepatitis Viruses Low tissue specificity: - Alphaviruses - Genus Flavivirus - Rabies virus

Question 123

Some humans have a genotype which protects them against infection by certain viruses. Name two human gene variations and the viruses against which they are protective as well as the putative underlying mechanisms.

Answer 123

HCV - Genetic variation in IL28B -> upstream region of IL28B gene = IFN gamma 3 = IFN class 3 molecule SARS-CoV - Trim 55

Question 124

What does the term “trans-infection” describe and in which virus system it was discovered?

Answer 124

A cell "holds" a pathogen without getting infected (the pathogen does not enter the cell), only to pass it to another cell to infect it -> HIV-1?

Question 125

Which alphavirus led to massive outbreaks in the human population since 2013? Name virus, main symptoms and route of transmission.

Answer 125

Chikungunya Virus -> ss (+) RNA - gehört zur Gruppe der Arboviren -> transmitted via Arthropodes - causes Chikungunya fever

Question 126

For which viruses RNA recombination events are part of their regular life cycle? List two viruses and briefly explain the individual role of the recombination event in the replication cycle.

Answer 126

FELINE CORONAVIRUS (FCoV) FeCoV -> RNA recombination, (non homologous) deletions -> FIP virus (Feline infectious peritonitis) - recombination leads to lethality of the disease -> before its an infection without massive symptoms ALPHAVIRUSES Eastern equine encephalitis virus (EEV) + Sindhis virus -> Western equine encephalitis virus (WEEV) -> leads to formation of a novel virus

Question 127

Explain the generation, the function/mode of action of the pr peptide during vision morphogenesis for members of the genus Flavivirus

Answer 127

pr = proteolytic product -> In the mature, infectious vision, the pr peptide is absent, and the virus undergoes membrane fusion in the end-some at low pH

Question 128

What is the FIP virus? Which disease is associated with this virus? What is unusual about this disease/pathogen?

Answer 128

= Feline Infektiöse Peritonitis - lethal disease - peritonitis and/or pleuritis - or granulomatosis in multiple organs Genomic sequence very similar to the Feline Panleucopenia which leads heart muscle degeneration

Question 129

What is the difference pathogenicity and virulence of a germ?

Answer 129

PATHOGENICITY - quality or state of being pathogenic -> the potential ability to produce disease -> qualitative term -> "ALL OR NONE" principle VIRULENCE - disease producing power of an organism - degree of pathogenicity within a group or species - term that "quantifies pathogenicity"

Question 130

The following statements about the capsid of picornaviruses are: Statement The capsid contains 60 copies each of proteins VP1 to VP4. VP2 and VP3 are located at the top of the 20 octamers (called molecular mountains). VP1 to VP3 are jelly roll barrel structures. VP4 is buried inside the capsid. Canyon binder drugs target VP1 and prevent uncoating of the viral capsid.

Answer 130

- The capsid contains 60 copies each of proteins VP1 to VP4. - VP4 is buried inside the capsid - Canyon binder drugs target VP1 and prevent uncaring of the viral capsid

Question 131

The capsid of tomato bushy stunt virus, with triangulation number T=3, is built up from 180 identical protein chains. The following statements are: Statement The capsid protein can be divided into 3 domains, called R, S and P. 180 P-domains make up 90 protrusions on the outer surface of the icosahedron. Capsid proteins adopt one out of three possible conformations. The P-domains arrange to generate 45 x 2-fold and 45 x pseudo-2- fold rotation axis. An icosahedron displays 12 x 5-fold, 20 x 3-fold and 30 x 2-fold rotation axis.

Answer 131

- The capsid protein can be divided into 3 domains, called R, S and P. - 180 P-domains make up 90 protrusions on the outer surface of the icosahedron. - Capsid proteins adopt one out of three possible conformations.

Question 132

The following statements about influenza virus neuraminidase (NA) are: Statement NA is cleaved by the tryptase Clara into two fragments, NA1 and NA2. The so-called fusogenic peptide is part of the NA1 fragment. NA is a sialidase (cleaves off sialic acid from glycoproteins) that can be inhibited by Oseltamivir (Tamiflu®). The receptor binding domain of NA2 displays a jelly roll barrel architecture. 3 NA molecules (4-bladed propellor each) form the functional biological unit, a e) homotrimeric enzyme.

Answer 132

- NA is a sialidase (cleaves off silica acid from a glycoproteins) that can be inhibited by Oseltamivir (Tamiflu)

Question 133

Link the statements on the left side with the proteins (by putting a cross in the columns). Multiple links are possible. Statement 1. Nuclear export of viral RNA 2. RNA/DNA-dependent DNA Polymerase 3. CD4 receptor binding to evoke receptor ubiquitination and degradation 4. Apobec3G 5. Azidothymidine(AZT) 6. RNAseH Domain 7. Proofreading 8. Ubiquitin ligase recruitment to degrade cellular cytidine deaminase 9. Crm1-Ran.GTP pathway 10. Regulator of viral RNA splicing 11. Gly-tRNAGly1 A Reverse Transcriptase B Rev protein C Vif protein

Answer 133

Reverse Transcriptase: RNase H domain Rev protein: Nuclear export of viral RNA Vif protein: APOBEC3G, Ubiquitin ligase recruitment to degrade cellular cytidine deaminase

Question 134

Name three viruses from the genus Flavivirus

Answer 134

- Yellow fever virus - Dengue virus - Tick borne disease

Question 135

What is the role of prM during maturation of the virions of these viruses? Describe this process and the role of prM.

Answer 135

- protection from fusion during budding; Turin cleaves prM into pr and M (in TGN)

Question 136

Which functions has the glycoprotein of the Vesicular Stomatitis Virus during the infection process?

Answer 136

Glycoprotein G is involved in receptor recognition at the host cell surface and then, after endocytosis of the vision, triggers membrane fusion via a low pH-induced structural rearrangement.

Question 137

For what purpose is VSV G therefore often used?

Answer 137

- maybe Immunogenicity Design for Next-Generation Vaccines

Question 138

Which of the hepatitis viruses frequently induce persistent infections?

Answer 138

- HBV - HCV

Question 139

Name for each tropism one viral example: (wrong answers will lead to the deduction of points) Neurotropic Pneumotropic Lymphotropic

Answer 139

Neurotropic Herpes viruses Pneumotropic Influenza virus Lymphotropic Eppstein Barr Virus

Question 140

What changes in the envelope proteins of Influenza A virus are know which lead to a change of the viral tissue tropism? Explain the observed mutations and their effect on the spread of the virus mutants in the host and compare it to the wild type virus.

Answer 140

Influenza virus contains an envelope protein, hemagglutinin (HA), which mediates binding and fusion. HA consists of two subunits, HA1 and HA2. HA1 misdates virus binding and HA2 mediates fusion. The receptor for HA1 is terminal silica acid of N- and O-linked glycans. Influenza virus binds to cells via an interaction between HA1 and silica acid. The virus is subsequently endocytosed, and the low pH of the endosome elicits fusion activity of HA2.

Question 141

State one viral example (virus and family) for each of the possible polarities.

Answer 141

APICALWest Nil Virus BASOLATERAL: Vesicular Stomatitis Virus, Crimean-Congo hemorrhagic fever virus

Question 142

Proteins using the GEP (general excretion pathway) may be translocated - while being synthesized (cotranslationally) - after termination of their synthesis - before termination of transcription of the corresponding gene

Answer 142

- while being synthesized (cotranslationally) - after termination of their synthesis

Question 143

The GEP os the only pathway that - transports soluble proteins into the periplasm - that integrates membrane proteins into the plasma Membrane - that integrates porins into the plasma membrane

Answer 143

NONE

Question 144

In some pathways, the GEP-dependent transport is regulated by - a GTPase - a system of two GTPases - is only regulated by ATPases

Answer 144

- a GTPase (FtsY)

Question 145

The GEP is usually able to transport - unfolded proteins - folded proteins - tRNAs

Answer 145

- unfolded proteins

Question 146

The periplasmic space of E.coli - is reducing and thus allows the formation of disulfide bridges - is ATP-rich and thus allows the folding of proteins - is free of soluble proteases, therefore misfiled soluble proteins need to be reimported into the cytoplasm for degradation

Answer 146

NONE

Question 147

For the maintenance of the outer membrane of E.coli - proteins with beta-barrel folds must be integrated - lipopolysaccharides must be translocated to the outer leaflet - cholesterol is translocated across the periplasm

Answer 147

- proteins with beta-barrel folds must be integrated - lipopolysaccharides must be translocated to the outer leaflet

Question 148

The translocation of nuclear-coded proteins into the matrix of mitochondria occurs with the direct involvement of - the TOM-complex - the TIM22-complex - mtHSP70

Answer 148

- the TOM-complex - the TIM22-complex - mtHSP70

Question 149

TIM 9/10 is a complex of the inter membrane space, which is essential for the - integration of carrier proteins into the inner membrane - the translocation of proteins into the matrix - the biogenesis of beta-barrel proteins of the outer membrane whos activity depends on the presence of - ATP - GTP - CTP

Answer 149

- integration of carrier proteins into the inner membrane - the biogenesis of beta-barrel proteins of the outer membrane - NONE

Question 150

Proteins of the matrix that do not fold properly are usually degraded - in the matrix - in the intermemrane space - in the cytoplasm

Answer 150

- in the matrix

Question 151

Describe briefly, step by step how proteins are retrieved by means of the KDEL receptor by concentrating on following points: Which conditions lead to the binding and which to the release of its ligand, which vesicle coats interact with the receptor through which compartments the receptor cycles. Start with the unloaded receptor.

Answer 151

1. unloaded KDEL in ER due to pH 7,2 - 7,4 2. KDEL packed into COP II vesicle for transport to cis-Golgi 3. cis-Golgi: binding of ligand to KDEL due to low pH (pH 6,5 - 6,8) 4. packing into COPI for transport to ER 5. release of ligand in ER (pH 7,2 - 7,4)

Question 152

Name the two ways discussed for the formation of secretory granules (dense core vesicles)

Answer 152

1. condensing vacuole 2. homotypic fusion

Question 153

For the fusion of a subgroup of synaptic vesicles with the plasma membrane a so-called "kiss-and-run" hypothesis has been formulated. What is the rational basis for the hypothesis and what is the principal difference of the "kiss-and-run" mode from a normal endocytosis - exocytosis cycle?

Answer 153

"kiss and run": the vesicle and the PM do not fuse but some small "pore" is opened to mix the both lumina, the vesicle is reusable "Normally" the vesicle and membrane are fused together completely.

Question 154

Describe the major differences between "fluid phase endocytosis" and "receptor-mediated endocytosis". Would the term "Pinocytosis" match to any of these processes, and if so, why?

Answer 154

1. fluid phase endocytosis: slow unspecific uptake of nutrients 2. receptor-mediated endocytosis: binding of specific ligand to receptor for uptake, fast (30 % per minute) 3. fluid-phase = Pinocytosis

Question 155

„Multivesicular bodies“ (MVB) can be part (of a degradation pathway / of a secretion pathway). They contain internal vesicles, into which (membrane proteins / soluble proteins) are sorted, which usually have been tagged before by a (monoubiquitination / sumoylation / polyubiquitination).

Answer 155

- of a degradation pathway - of a secretion pathway - membrane proteins - monoubiquitination - polyubiquitination

Question 156

The following parts of a cell can be selectively targeted by autophagy (peroxisomes / mitochondrial ribosomes / midbodies). During formation of the autophagosome in macroautophagy lipids in the phagophore are (modified via O-glycosylation / modified via ubiquitination / enriched in sphingomyelin). In chaperone-mediated autophagy (only small organelles are digested / chaperones located in the lysosomal lumen are involved / cytoplasmic ATPases are involved).

Answer 156

- peroxisomes - midbodies - NONE - chaperones located in the lysosomal lumen are involved

Question 157

Name three fundamental mechanisms that are responsible for the asymmetric distribution of lipids between the leaflets of the plasma membrane

Answer 157

1. Flippase / active transport of PS and PE 2. asymmteric biosynthesis 3. unspecific transport

Question 158

Which are the two main pathways for delivery of lipids from the ER to the TGN?

Answer 158

- ER-TGN contact sites - vesicles

Question 159

During cytokinesis the new plasmamembanes are formed (before disassembling of the actin ring / under involvement of ESCRT-proteins / after division of the midbody into two equal pieces) The source of the additional membrane needed is mainly from (the outer mitochondria membrane | the peroxisome | the outer shell of lipid droplets). During open mitosis, the disassembling of the nuclear membrane requires (the phosphorylation of proteins of the nuclear lamina / the proteolysis of the nuclear pore / the transformation of sheet-like ER into tubular ER). ER-stacks in professional secretory cells like B-cells are only stable in the presence of (tight junctions / neurofilaments / ER-cisGolgi contact sites).

Answer 159

- under involvement of ESCRT-proteins - the outer shell of lipid droplets - the proteolysis of the nuclear pore - the transformation of sheet-like ER into tubular ER NONE

Question 160

Which function have sno/scaRNA during ribosome biogenesis? Where in the cell do they perform this function precisely? Are members of these RNAs also involved in the biogenesis of other RNPs and if so of which ones?

Answer 160

- scaRNA for snRNA processing in Cajal bodies - snoRNA part of RNP complex (RNA modification) in nucleoplasm

Question 161

Which of the following statements about the capsid of human rhino virus is/are correct/wrong? Multiple answers are possible. a) The capsid triangulation number T equals 4 (T=4) b) The icosahedron shell displays 12 x 5-fold, 20 x 3-fold and 30 x 2-fold rotation axes. c) The capsid contains 60 copies each of proteins VP1 to VP4. d) VP4displaysajelly-roll-barrelstructure. e) 5 copies of VP1 form the so-called "molecular mountains". f) Canyon-binder drugs target VP1 and prevent uncoating of the viral capsid.

Answer 161

b) The icosahedron shell displays 12 x 5-fold, 20 x 3-fold and 30 x 2-fold rotation axes. c) The capsid contains 60 copies each of proteins VP1 to VP4. e) 5 copies of VP1 form the so-called "molecular mountains". f) Canyon-binder drugs target VP1 and prevent uncoating of the viral capsid.

Question 162

2. Which of the following statements about Bacteriophage MS2 is/are correct/wrong? Multiple answers are possible. a) The icosahedron shell is made up of a single type of coat protomer. b) The viral RNA-genome contains a so-called packaging signal. c) The coat protomer posesses a jelly-roll-barrel structure. d) TheMS2coatprotomerformsahomodimer. e) The coat protomer posesses a chymotrypsin-like fold. f) The capsid triangulation number T equals 3 (T=3).

Answer 162

a) The icosahedron shell is made up of a single type of coat protomer. b) The viral RNA-genome contains a so-called packaging signal. d) TheMS2coatprotomerformsahomodimer. f) The capsid triangulation number T equals 3 (T=3).

Question 163

Which of the following statements about the Influenza virus Neuranimidase (NA) and Hemagglutinin (HA) is/are correct/wrong? Multiple answers are possible. a) HA is cleaved by the host cell tryptase Clara into two fragments, HA1 and HA2 b) The so-called fusogenic peptide, exposed at low/acidic pH, is part of the HA2 fragment. c) NA displays muraminidase activity that can be inhibited by β-Lactam-Antibiotics. d) 4 NA molecules, each displaying a 4-bladed propeller, form the functional biological unit e) Fusion Inhibitors affect HA fragment 6-helix-bundle formation, which is mandatory for infectivity. f) Many non-enveloped viruses typically possess a fusion glycoprotein that harbours HA1 - HA2 segments.

Answer 163

a) HA is cleaved by the host cell tryptase Clara into two fragments, HA1 and HA2 b) The so-called fusogenic peptide, exposed at low/acidic pH, is part of the HA2 fragment. d) 4 NA molecules, each displaying a 4-bladed propeller, form the functional biological unit e) Fusion Inhibitors affect HA fragment 6-helix-bundle formation, which is mandatory for infectivity.

Question 164

Statements about GP120, Reverse Transcriptase, Vif protein, Rev protein

Answer 164

GP120: CD4 receptor binding to evoke receptor ubiquitination and degradation Reverse Transcriptase: RNAseH Domain, tRNA(Lys3) Vif protein: Ubiquitin ligase recruitment to degrade cellular cytidine deaminase Rev protein: Crm1 - Ran.GTP - eIF-5A export pathway, Regulator of viral RNA splicing

Question 165

At which membrane does the budding of retroviruses occur?

Answer 165

plasma membrane

Question 166

Which cellular pathway and protein complexes are involved in retroviral budding? State the names of the pathway and protein complexes.

Answer 166

- ESCRT complex - VPS pathway (vacuolar protein sorting)

Question 167

(+)-strand RNA viruses restructure the intracellular membrane systems of the host cell for their genome replication. Name for each of the compartments listed below one virus which makes use of these membranes for genome replication:

Answer 167

ER: HCV Golgi: Kunjivirus Lysosomen: Rubella/Alphavirus Mitochondrien: Flock house virus

Question 168

By which method were 3D models of the virus-induced membrane structures obtained? Describe the basic methodology in catchwords (name and principle).

Answer 168

electron microscopy/tomography and 3D modeling

Question 169

For viruses restructuring the ER two basic models/mechanisms how the membrane spherules are generated were postulated based on these analyses. Name the two models/mechanisms and give for each one a viral example.

Answer 169

- via invagination - via MVB

Question 170

Explain why a certain cell type is required for such a study (polarity of a virus). Name cell type and its specific features.

Answer 170

tight junctions

Question 171

State one viral example (virus and family) for each of the possible polarities.

Answer 171

apical: Influenza A basolateral: Herpesviruses

Question 172

What is the in vivo relevance of the polarity in virus release?

Answer 172

hide from immune system

Question 173

Viruses take active counter measures against the interferon induction via the RIG-I pathway. Give one example of a (+)-strand and one example of a (-)-strand RNA virus and explain which viral proteins are used to antagonize their recognition by this pathway. Name the viral antagonists and their mode of action.

Answer 173

- Influenza A (-ssRNA) NS1 binds TRIM25 -> no ubiquitination of RIG-1, no binding to IPS-1 -> no interferon - HCV NS3-4A inhibits MAVS (IPS-1)

Question 174

Explain the generation, the function/mode of action of the pr peptide during virion morphogenesis for members of the genus Flavivirus.

Answer 174

non mature virions -> no membrane fusion/ budding cause pr (helper protein) binds to E pr proteolytical cleaved but stays at E cause low pH in endosomes/vesicle neutral pH in extracellular milieu, release of E, conformation chance -> fusion peptide active -> budding

Question 175

A minority of viruses utilize non-canonical mechanisms in the biogenesis of miRNA molecules. Which of the following answers is/are correct/wrong? some viral pre-miRNAs are transcribed by RNA polymerase III all viral miRNA precursors are transcribed by RNA polymerase II all viral pre-miRNAs are exported into the cytoplasm by exportin-5 all viral pre-miRNAs are exported into the cytoplasm by exportin 1 (Crm1) all viral miRNA precursors are processed by drosha all viral pre-miRNAs are processed by dicer

Answer 175

- some viral pre-miRNAs are transcribed by RNA polymerase III - all viral pre-miRNAs are exported into the cytoplasm by exportin-5 - all viral miRNA precursors are processed by drosha all viral pre-miRNAs are processed by dicer

Question 176

Der SecY-abhängige post-transnationale Transport von Proteinen über den General Excretion Pathway (GEP) verwendet als Energiequelle - ATP - die PMF - GTP

Answer 176

- ATP - die PMF

Question 177

Der GEP ist beteiligt an der - Sekretion von Proteinen mittels Autotransportern - beim TAT-Transportweg - bei der Biogenese von Typ I Pili

Answer 177

- Sekretion von Proteinen mittels Autotransportern - bei der Biogenese von Typ I Pili

Question 178

Typ III Sekretion benutzt einen makromolekularen Komplex - der drei Membranen durchqueren kann - der homolog zu Teilen bakterieller Flanellen ist - der ausschließlich co-translational funktioniere

Answer 178

- der drei Membranen durchqueren kann - der homolog zu Teilen bakterieller Flanellen ist

Question 179

Die Typ-I-Sekretion verwendet als ATPasen Vertreter der - ABC-Transporter - der AAA-ATPasen - der F0/F1-ATPasen

Answer 179

- ABC Transporter

Question 180

Der Import von Proteinen in die Matrix der Mitochondrien verwendet eine - saure - amphipatische - hydrophobe Signalstruktur, die in Gegenwart ihres Rezeptors - eine Helix - eine beta-Faltblattstruktur - ein sogenanntes beta-barrel bildet

Answer 180

- amphipatische - eine Helix

Question 181

Das Mitochondriengenom der Säuger codiert für - Proteine der äußeren Mitochondrienmembran - Proteine der inneren Mitochondrienmembran - tRNAs der Matrix

Answer 181

- Proteine der inneren Mitochondrienmembran - tRNAs der Matrix

Question 182

Im Zellkern codierte Säugerproteine der inneren Membran, die ein internes Targetingsinal besitzen, nutze zur Insertion - den TOM-complex - den TIM22 complex - das mtSecY

Answer 182

- den TOM-complex - den TIM22 complex

Question 183

Lückentext ER und Golgi Transport

Answer 183

Der COP II coat ist am Transport vom ER zum GOLGI beteiligt. Der KDEL-Rezeptor dient der Rückführung von Proteinen aus dem GOLGI zum ER. Der Import von Zuckern in den Golgi erfolgt mittels ANTIPORTERN. In Säugerzellen befinden sich die ER-exit sites ÜBER DAS ER NETZWERK VERTEILT Ein entscheidender Auslöser für die Aktivierung von Proteinkonvertasen ist der im Verlauf des sekretorischen Weges ÄNDERUNG pH-Wert im Lumen.

Question 184

Synaptische Vehikel der Säuger haben normalerweise einen Durchmesser von - 2 nm - 2 µm - 2 mm

Answer 184

NONE

Question 185

Die Fusion der Vesikel wird durch den Einstrom von ................. Ionen getriggert.

Answer 185

-Ca2+

Question 186

Tetanusneurotoxin hemmt die Fusion synaptischer Vesikel .................. eines SNARE Proteins

Answer 186

proteolytic cleavage

Question 187

Die Endocytose von Rezeptoren kann - mittels Clathrine coats - mittels Calveoline - mittels Coatamer erfolgen

Answer 187

- mittels Clathrine coats - mittels Calveoline

Question 188

Was beschreibt der Begriff "kompensatorische Endozytose"?

Answer 188

den Erhalt einer konstanten PM-Oberfläche durch Endocytose bei starker Exocytose

Question 189

Lückentext Lysosomen, Vesikel, endocytose

Answer 189

Die Ablösung endocytierter Giganten von ihren Rezeptoren in endosomalen Kompartimenten erfolgt auf Grund der Änderung DES PH WERTES im Lumen der Kompartimente. In Säugerzellen erfolgt das Targeting vieler Enzyme zum Lysosomen über MANNOSE-6-PHOSPHAT. Der spezifische Abbau von Lipidvesikeln in Lysosomen wird ermöglicht durch die schützende Wirkung der GLYCOCALYNX auf die Grenzmembran der Lysosomen und die destabilisierende Wirkung von LBPA/BMP auf die internalisierten Membranvesikel.

Question 190

Beschreiben Sie in drei Hauptphasen der Zytokinese bei Säugerzellen.

Answer 190

1. begin of assembly of constriction ring at the PM (middle of cell) 2. Midbody formation by actin-myosin ring 3. Absission: disassembly of ring and sealing of PM

Question 191

- Im Rahmen der "organellar inheritance" während der Mitose fusionieren große Teile des Golgi-Apparates mit dem Endosomal/lysosomalen Kompartiment - Bei der Teilung der Chloroplasten wird zuerst das Membransystem der Thylakoide, dann die innere Membran und zum Schluss die äußere Membran geteilt. - Die homonymische Fusion von Mitochondrien der Säugerzellen erfolgt mittels SNARE- Proteinen.

Answer 191

- Bei der Teilung der Chloroplasten wird zuerst das Membransystem der Thylakoide, dann die innere Membran und zum Schluss die äußere Membran geteilt. - Die homonymische Fusion von Mitochondrien der Säugerzellen erfolgt mittels SNARE- Proteinen.

Question 192

Neben rRNA, tRNA und mRNA haben eukaryonitsche Zellen verschiedene evolutionär konservierte sogenannte "kleine RNAs". Nennen sie drei Beispiele hochkonservierter Arten und ihre Funktion in der Zelle

Answer 192

1. snRNA: Spleißosome 2. snoRNA: part of RNP complex 3. 7SLRNA: SRP (signal recognition particle)

Question 193

Sie wollen ein Matrixprotein des Schweines mittels cDNA rekombinant in einer Bakterienzelle explizieren und dabei erreichen, dass es sekretiert wird. Welche Veränderungen müssen Sie vornehmen?

Answer 193

- mitochondrial matrix import signal removal - bacterial export signal (secDF, SecY) adding

Question 194

Aussagen über VP1, VP2/3, VP4

Answer 194

VP1: Myristylated, Canyon binder, Capsid 5-fold symmetry axis, Capsid molecular mountain-top, Capsid outside surface, Jelly role topology VP2/3: Capsid 5-fold symmetry axis VP4: Capsid pseudo 6 fold axis, Capsid asymmetric axis

Question 195

Verschiedene Aussagen über Influenza A

Answer 195

- The so-called fusogenic peptide is part of the membrane-anchored HA2 fragment - HA is a sialidase that can be inhibited by Oseltamivir (Tamiflu)

Question 196

Verschiedene Aussagen über HIV-1 reverse transcription

Answer 196

- A single vRNA strand contains two LTRs, each consisting of a U3-, R- and U5-region. - RT is a dimeric protein that tabours only one Nase-H domain. - Reverse transcription can be inhibited by nucleoside and non nucleosidic inhibitors - Provirus integration into the hosts Genome is at the cost of a 2-basepare loss in the U5 region of each of the two LTRs.

Question 197

The incubation time after the bite by a rabies infected dog is up to

Answer 197

several months

Question 198

Describe the individual steps of the spread of rabies infection after inoculation into a muscle of a person's leg

Answer 198

muscle -> peripheral NS -> ganction -> spinal cord -> brain -> CNS -> death

Question 199

Name two viruses (virus and family) whose infection occurs via the gastro intestinal tract

Answer 199

Reoviridae: Rotavirus, Orbivirus -> BVDV Coronavirus (Pigs) Norovirus -> Caliciviridae

Question 200

Which special property is essential for this viral life style (besides suitable receptor usage) for gastro intestinal viruses?

Answer 200

cellular transcription factors are essential for viral promoter

Question 201

Which specialized cells in the gastro intestinal tract play an important role in some of those infections and what is the special property of those cells?

Answer 201

- M cells - M cells take up antigens and present them to lymphocytes which are located below - but some viruses use M-cells for entry and spreading (Reovirus, Poliovirus) or infection and replication (Rotavirus)

Question 202

What does the abbreviation "GALT" stand for?

Answer 202

Gut associated lymphoid tissue

Question 203

Täterin (CD317) exerts an antiviral role. Against which virus family does it act and what is the antiviral mechanism?

Answer 203

Retroviruses (budding via ESCRT pathway) (envelope) - Tetherin in virus membrane bins to Tetherin of CD317 in host membrane - no budding - vesicle isn't released - uptake of virus into the cell and degradation in lysosome

Question 204

Name three cellular sensors for "foreign" RNA and describe their substrate specificity.

Answer 204

- dsRNA - hairpin structure in RNA - 5' Triphosphate

Question 205

Explain shortly the terms and molecular basis of "antigenic shift" and "antigenic drift" in the context of the influenza virus system.

Answer 205

DRIFT - partial immunity possible, normal immune response, new variant (mutations) -> seasonal ("die schon wieder" = drift) SHIFT - zoonosis (animal -> human), no immunity in host, overreaction of immune system, unpredictable/fatal - pandemic (bop Spanische Grippe shift)

Question 206

Describe the two models for the mechanism of RNA recombination

Answer 206

HOMOLOGOUS between two partners with significant sequence homologies (asp two polioviruses) NON HOMOLOGOUS between partners with no significant sequence homologies (virus and mRNA host)

Question 207

Name two RNA viruses for which the process of RNA recombination is an ESSENTIAL step in the regular replication cycle?

Answer 207

Orthomyxoviridae - Influenza A (cap-snatching) Nidovirales - Coronavirus (discontinous transcription)

Question 208

Explain the priming reaction of the reverse transcription of hepatitis B virus. Name the involved molecules

Answer 208

5' epsilon stem loop - p binds to UUC in epsilon for primer synthesis (Nucleotide primer AAG) - switch to 3' DR1 sequence - Elongation

Question 209

Course of infections

Answer 209

Acute infection -> e.g. Influenza virus, Rhinovirus Chronic infection -> e.g. Hepatitis C virus Latent infection -> e.g. herpes simplex virus (HSV) Slow infection -> e.g. HIV

Question 210

Der general excretion pathway (erlaubt in vielen Fällen die Sekretion von gefallteten Proteinen / überquert bei den… auch die äußere Membran / ist homolog zum Proteintransport über das ER)

Answer 210

- erlaubt in vielen Fällen die Sekretion von gefallteten Proteinen - ist homolog zum Proteintransport über das ER

Question 211

YidC bzw. homolge dieses Proteins (unterstützen den Transport von Membranproteinen/ und ATPasen/ findet man auch in der inneren Membran von Mitochondrien und der Thylakoidmembran von Plasmiden)

Answer 211

- unterstützen den Transport von Membranproteinen - findet man auch in der inneren Membran von Mitochondrien und der Thylakoidmembran von Plasmiden

Question 212

Der TAT-Transportweg (ist GTP abhängig / transportiert gefaltete Substrate / erkennt beim Trgeting ein hydrophobes Signal am N-terminus des Substrates )

Answer 212

-transportiert gefaltete Substrate - erkennt beim Targeting ein hydrophobes Signal am N-terminus des Substrates

Question 213

Die Knüpfung von Disulfidbrücken in Proteobakterien (E.coli) (erfolgt fast nur im Periplasma / beinhaltet eine Elektronentransportkette ohne lösliche Faktoren / führt zur Ausbildung von kovalent verbundenen Intermediaten aus Substrat und Disulfidisomerasen)

Answer 213

- erfolgt fast nur im Periplasma - führt zur Ausbildung von kovalent verbundenen Intermediaten aus Substrat und Disulfidisomerasen

Question 214

Die für eine Isomerisierung notwendigen Elektronen kommen (immer über die Atmungskette von Sauerstoff / nur unter aeroben Bedingungen vom Sauerstoff / in der Regel immer über Thioradoxin von NADPH).

Answer 214

- in der Regel immer über Thioradoxin von NADPH

Question 215

Das DegP des Periplasmas agiert während der Biogenese von Proteinen der äußeren Membran als (Chaperon / Protease / Peptidylprolylisomerase).

Answer 215

- Chaperon - Protease

Question 216

Das Importsignal für mitochondriale Matrixproteinen in Säugern ist eine (amphiphatische Helix / derigiert das Protein durch den TIM22-Komplex / wird häufig nach dem durchqueren der äußeren Membran im Intermembranraum abgeschnitten)

Answer 216

amphiphatische Helix

Question 217

Der Import von Proteinen aus dem Zytoplasma in Plastiden über den TOC-Komplex (erfolgt oft co-translational / benötigt kein GTP / benötigt ausschließlich ARP im Stroma)

Answer 217

NONE

Question 218

Wie wird verhindert, das ER-residente Membranproteine durch den Vesikeltransport aus dem ER verloren gehen? Nennen sie die zwei Hauptmechanismen und – so vorhanden – typische Primärstrukturen, die diese Mechanismen steuern.

Answer 218

Retention z.B. durch Interaktion mit Ribosomen Rücktransport über Interaktion mit COPI-coat Kkxxcooh oder (nh2)XXRR

Question 219

Nennen sie drei Hauptstadien bzw. wichtige Schritte der Biogenese sekretorischer Granula und ihrer Inhalte (Typ dense core vesicle) entsprechend dem „condensing vauole“ Modell.

Answer 219

1. Abschnürren eines großen Bereiches aus dem TGN 2. Ansäurung, Abschnürung vo Vesikel nicht zum SG gehörenden Proteinen zum Endosom 3. Reifung der Proteininhalte (Processing von Pro-Sequencen) 4. Andocken an die Plasmamembran

Question 220

Bei der Reifung von Endosomen kann Material aus dem späten Endosomen (zum TGN / zum Lysosomen / zum sorting endosome) gelangen.

Answer 220

- zum TGN - zum Lysosomen

Question 221

Receptor down regulation erfordert als ersten Schritt (eine Neddylierung / eine Sumoylierung / eine Acetylierung) des zatoplasmatischen Teils des Proteins.

Answer 221

NONE

Question 222

Das Mannose-6-Phophat Signal (wird endgültig im Golgi geformt / kann Proteine von der Plasmamembran in das Lysosome dirigieren / binder bei leicht saurem pH-Wert an seinen Rezeptor).

Answer 222

- wird endgültig im Golgi geformt - kann Proteine von der Plasmamembran in das Lysosome dirigieren - binder bei leicht saurem pH-Wert an seinen Rezeptor

Question 223

Macroautophagy (dient u. a. Der Glucosemobilisierung durch Abbau von Glycogranula / ist im Gegensatz zur Mikroautophagy nie selektiv hinsichtlich des Abbaus bestimmter Organellen / benutzt überwiegend Plasmamembranbereiche zur Formierung der Grenzmembran (limiting membrane)).

Answer 223

- dient u. a. Der Glucosemobilisierung durch Abbau von Glycogranula

Question 224

Exosomen sind (Vesikel, die durch Fusion später Endosomen bzw. Lysosomen freigesetzt werden / stehen im Verdacht, RNAs von Zelle zu Zelle transportieren zu können / sind von einer Glycokalyx aus LAM Proteinen umgeben)

Answer 224

- Vesikel, die durch Fusion später Endosomen bzw. Lysosomen freigesetzt werden - stehen im Verdacht, RNAs von Zelle zu Zelle transportieren zu können

Question 225

Ein Kontakt zwischen zwei Kompartimenten, bei dem sich eine Fusionspore bildet, die Durchmischung der Lumina erlaubt, die Durchmischung der Grenzmembrane aber im wesentlich verhindert bzw. verzögert wird oft als „kiss and run“-Mechanismus bezeichnet. Nennen sie zwei zelluläre Vorgänge, bei denen solch ein Mechanismus dikutiert wird.

Answer 225

Exocytose synaptischer Vesikel Stofftransport zwischen spätem Endosom und Lysosom

Question 226

Welche Ursachen hat die asymetrische Lipidverteilung zwischen der äußeren und der inneren Lipidshchicht der Plasmamembran der Säuger?

Answer 226

Assymetrie in der Lipidverteilung in den exocytotischen Vesikeln Fehlen von Transportern e.g. für Glycolipide und Sphingolipide Aktiver Transport von Aussen nach Innen für PE und PS

Question 227

In der ersten Phase der Zytokinese bei Säugerzellen erfolgt die Formierung einer ringförmigen Struktur aus (Aktin / Myosin / Tubulin) unterhalb der Plasmamebran.

Answer 227

- Aktin - Myosin

Question 228

Die Auflösung der Kernhülle während des Zellzyklus (wird verhindert durch die Phosphorylierung von Komponenten der Kernpore und der Kernlamina / wird unterstützt durch Mikrotubuli / beinhalte das Zerfallen der Kernporen in Subkomplexe)

Answer 228

- wird unterstützt durch Mikrotubuli - beinhalte das Zerfallen der Kernporen in Subkomplexe

Question 229

Das an der Fusion von Mitochondrien beteiligte mitofusin (Fzo1) ist (homolog zu SNARE-Proteinen / strukturell analog zu SNARE-Proteinen / weist keine Ähnlichkeit zu SNARE-Proteinen auf).

Answer 229

- strukturell analog zu SNARE-Proteinen

Question 230

In folgenden RNA-Molekülklassen können post-transkriptional Basen modifiziert werden (rRNA / mRNA / miRNA)

Answer 230

- rRNA - mRNA

Question 231

Polyadenylierung führt bei folgenden Molekülen i der Regel nicht zum Abbau (eukaryontischer prä-5srRNA / prokaryontische mRNA / prokaryontische prä-tRNA)

Answer 231

NONE

Question 232

Nennen sie drei Eigenschaften / Primärstrukturelemente in eukaryontischen mRNAs, die Einfluß auf ihre Halbwertszeit haben können:

Answer 232

Länge Poly-A Vorkommen ARE Vorkommen premature Stop

Question 233

A) Clara B) Neuraminidase C) Hemagglutinin D) M2 protein 1. Angiotensin Converting Enzyme II 2. RT-Polymerase 3. Oseltamivir (Tamiflu) 4. High pH form with substrate binding domains (a jelly roll) on top (exposed) 5.Tetramer of 6-bladed β-propeller structure 6. Hydrolyses HA to form HA1 and HA2 7. Pentameric structure 8. Viral glycoprotein 9. Low pH form exposig the fusogenic peptide for membrane insertion 10. Sialidase 11. Tryptase 12. An acid-activated channel

Answer 233

Clara: 6. Hydrolyses HA to form HA1 and HA2 11. Tryptase Neuraminidase: 3. Oseltamivir (Tamiflu) 5.Tetramer of 6-bladed β-propeller structure 8. Viral glycoprotein 10. Sialidase Hemaglutinin: 4. High pH form with substrate binding domains (a jelly roll) on top (exposed) 8. Viral glycoprotein 9. Low pH form exposig the fusogenic peptide for membrane insertion M2 protein: 12. An acid-activated channel

Question 234

A) Picornaviruses B) Bacter Bacteriophage MS2 C) Tobacco mosaic virus 1. Triangulation number T = 3 2. 16 coat protein per helicasl turn 3. jellyy roll of 6 β-strands and a Greek key motif 4. Coat protein dimer recognize RNA packing signal 5. small genome encodes 4 proteins only 6.3 copies each of VP1 and VP2 arrange around pseudo 6-fold rotation axes 7. 60 copies each VP1 and VP4 8. Total of 8 x 5-fold, 12 x 3-fold and 16 x 2-fold axes 9. 20 identical equilateral triangular tiles 10. Diploid DNA-RAN hybrid genome 11. Canyon binder drugs 12. A few thousand coat protein copies make up the capsid

Answer 234

Picornaviruses 1. Triangulation number T = 3 3. jellyy roll of 6 β-strands and a Greek key motif 7. 60 copies each VP1 and VP4 9. 20 identical equilateral triangular tiles 11. Canyon binder drugs Bacter Bacteriophage MS2 1. Triangulation number T = 3 4. Coat protein dimer recognize RNA packing signal 5. small genome encodes 4 proteins only Tobacco mosaic virus 2. 16 coat protein per helicasl turn 12. A few thousand coat protein copies make up the capsid

Question 235

Infections with enteroviruses inuce the expression of the cellular miR-141 in the infected cells. Which statements are correct? (ROT = RICHTIGE ANTWORT) a) the virus-induced expression of cellular miR-141 reduces the expression of cellular eIF4E protein by degradation of eIF4E-mRNA b) the virus-induced expression of cellular miR-141 reduces the expression of cellular eIF4E protein by inhibiting of eIF4E-translation c) the virus-induced expression of cellular miR-141 reduces the expression of cellular eIF4E protein by inhibiting of eIF4G-translation d) the virus-induced expression of cellular miR-141 reduces the expression of cellular eIF4E protein by degradation of eIF4G-mRNA e) the virus-induced expression of cellular miR-141 reduces the cap-dependent translation of cellular mRNAs f) the virus-induced expression of cellular miR-141 decreases the cap-dependent translation of enteroviral RNA

Answer 235

b) the virus-induced expression of cellular miR-141 reduces the expression of cellular eIF4E protein by inhibiting of eIF4E-translation e) the virus-induced expression of cellular miR-141 reduces the cap-dependent translation of cellular mRNAs

Question 236

. A minority of viruses utilize non-canonical mechanisms in the biogenesis of miRNA molecules. A) Which statements are correct? a) some viral pre-miRNAs are transcribed by RNA polymerase III b) all viral miRNAs are transcribed by RNA polymerase III c) all viral pre-miRNAs are exported into the cytoplam by exportin-5 d) all viral pre-miRNAs are exported into the cytoplam by exportin 1 (Crm1) e) all viral miRNAs precursors are processed by drosha f) all viral pre-miRNAs precursors are processed by dicer

Answer 236

a) some viral pre-miRNAs are transcribed by RNA polymerase III c) all viral pre-miRNAs are exported into the cytoplam by exportin-5 f) all viral pre-miRNAs precursors are processed by dicer

Question 237

The biogenesis of ouse gammherpesvirus 68 (MHV 68) and bovine leukemia virus (BLV) encoded miRNAs differ from the main miRNA biogenesis pathway. Name the two common differences.

Answer 237

Both transcribed by RNA pol III Don’t need drosha processing

Question 238

Name two viruses with very narrow and two with very broad host range (virus and family) and their host species.

Answer 238

Narrow: HBV (Hepadnaviridae), HCV (Flaviviridae), HAV (Picornaviridae) Broad: Dengue (Flaviviridae), Rabies virus (Rhabdoviridae)

Question 239

First name the three categories of host factors (not individual proteins) which determine the host or tissuse specificity of viruses and then give one example for each category.

Answer 239

1. Receptor: Polio-Rezeptor (CD155), mouse with receptor permissive for PV 2. Cellular factors for viral replication: miR122, HCV RNA replication 3. Cellular factors for virus maturation: ApoB, HCV virion morphogenesis

Question 240

What is the role of the prM in the maturation of virions of the genus Flavivirus? Explain the fate and function of prM during virion morphogensis

Answer 240

prM has to protect E from premature fusion during assembly and budding process prMis cleaved by Furin in the TGN into pr and M; pr remains bound to E due to the low pH in the TG and the secretory pathway and shields fusion loop of E after budding in neutral pH is released and allows the fusion loop to act in infection

Question 241

Give a short explanation for them terms „genetic shift“ and „genetic drift“ in the context of Influenza virus. What special requirement is prerequisite for one of these two mechanisms?

Answer 241

Antigenic drift: small sequence variations by erors of the viral RdRp Antigenic shift: drastic sequence change by the exchange of a genome segment Due to double infection of a single cell by two different Flu viruses. Term: Reassortment of segmented genomes

Question 242

Describe briefly the individual steps after the release of a newly formed influenza A virus until to the release of its genome into a newly infected cell.

Answer 242

Virus needs to detach from the cell and uses Neuramidase Enzyme/protein to get away from the parental cell HA needs to be cleaved by a host protease (like proteinase Clara from Clara cell) into HA1 and HA2 The infectious virus binds to sialic acids attached to cellular prteins This leads to the uptake of the virus into clathrine coated endosomes Uppon accidification HA trimer undergoes a conformational change and the virus membrane and the endodsomal membrane fuse, leading to the release of the genome segments into cytoplasm

Question 243

. Influenza A virus can block the induction of interferon alpha/beta with one of its gene products. Explain based on a scheme the underlying molecuar mechanism (which viral gene product, which celular signaling molecule, how is the signaling chain interrupted).

Answer 243

Influenza A virus nonstructural protein (NS1) sepcifically inhibits TRIM25-mediated RIG-I CARD ubiquitination, thereby suppressing RIG-I signal transduction.

Question 244

) The budding of retroviruses occurs: a) ER membrane b) Plasma membrane c) Intermediate compartment d) Golgi membrane

Answer 244

b) Plasma membrane

Question 245

Which cellular protein complexes are used by retroviruses for assembly and budding (correct full name and abbreviation).

Answer 245

ESCRT-protein complex (endosomal sorting complex required for transport)

Question 246

List two different cellular proteins for these complexes which undergo interactions with two retroviral proteins during budding.

Answer 246

ALIX, TSG101

Question 247

RNA recombination: A) Describe by catchwords and a scheme the two models for the mechanism of RNA recombination.

Answer 247

Breakage and ligation Template shift

Question 248

For which RNA viruses is the process of RNA recombination an essentiell step in the replicaion cycle? Explain two examples by using catchwords.

Answer 248

Influenza: cap snatching Corona/Nidovirusess: Leader primed / discontinuous transcription

Question 249

What are „Negri bodies“, where are they detected, what are they composed of and for which viral infection are they an Indication?

Answer 249

Histopathologial changes associated with rabies encephalitis Pyramidal cells of Ammon’s horn; Purkinje cells of the cerebellum, medulla and various other ganglia Contain rabies N + M protein and TLR3

Question 250

Viruses use cellular filopodia for cell spread. Name 3 viruses from different families and explain the mechanistic differences in their use of the filopodia for cell to cell spread.

Answer 250

a) Newly formed retroviruses accumulate on the cell surface, they surf on existing filopodia and are transported via retrograde transport on filamentous actin to the new target cell b) long contact between target membrane and filopodia leads to their uptake, facilitates virus transmission followed by intracellular actin driven transport c9 vaccinia virus: induces from outside the formation of actin-"comet tail", virus is thereby transported toward target cell , actin-flow in the target cell is used for further transport processes d) African swine fever virus, induces from inside the formation of filopodia

Question 251

Which of the following statements concerning capsides and envelopes of RNA-viruses are NOT correct? - The envelope and the capsid of enveloped RNA-viruses usually contain (at least) one glycoprotein, one matrix protein and one nucleocapsid protein. - The outer envelope of the influenza virus contains one transmembrane channelpermeable for protons. - The capsid of alpha viruses consists of a protease-degrading itself by autolysis after binding to a receptor on the host membrane, thus enabling the entrance of viral RNA into the host cell. - The capsid of picorna viruses consist of 60 copies each of the proteins VP1, VP2, VP3 and VP4. Of these, VP1, VP2 and VP3 possess a "jelly roll"-fold - The capsid of picorna viruses exhibits a dodecahedral-symmetry.

Answer 251

- The capsid of alpha viruses consists of a protease-degrading itself by autolysis after binding to a receptor on the host membrane, thus enabling the entrance of viral RNA into the host cell. - The capsid of picorna viruses exhibits a dodecahedral-symmetry.

Question 252

Which of the following statements concerning capsids and envelopes of RNA-viruses are NOT correct? - The capsid of picorna viruses consists of twelve pentamers of the composition (VP1, VP2, VP3, VP4). - The capsid of picorna viruses consists of twenty trimers of the composition (VP1, VP2, VP3, VP4). - The capsid of picorna viruses consists of thirty dimers of the composition (VP1, VP2, VP3, VP4). - The processing of the picorna viral poly protein P1 in the mature capsid proteins VP1, VP2, VP3 and VP4 is performed by the viral protease 2A. - "Canyonbinders" are hydrophobic compounds binding in a cavity of the picornaviral capsid surrounding the VP1-pentamer.

Answer 252

- The processing of the picorna viral poly protein P1 in the mature capsid proteins VP1, VP2, VP3 and VP4 is performed by the viral protease 2A.

Question 253

What are the mechanistic features of the miR-122 function during HCV replication? Which statements are correct? - The cellular miR-122 binds to the 3' UTR and to the 5' UTR of the viral genome. - The binding sites for the cellular miR-122 are exclusively located in the 5' UTR of the viral genome. - The mode of action of the cellular miR-122 on HCV replication mainly based on the inhibition of translation of the viral RNA by binding to the 3' UTR of the viral RNA. - The mode of action of the cellular miR-122 on HCV replication is mainly based on the increase of stability of the viral RNA by binding to the 3' UTR of the viral RNA. - The mode of action of the cellular miR-122 on HCV replication is mainly based on the increase of stability of the viral RNA by binding to the 5' UTR of the viral RNA. - The mode of action of the cellular miR-122 on HCV replication is only based on the negative regulation of translation of cellular liver-specific mRNAs by binding to their 3' UTRs.

Answer 253

- The cellular miR-122 binds to the 3' UTR and to the 5' UTR of the viral genome. - The mode of action of the cellular miR-122 on HCV replication is mainly based on the increase of stability of the viral RNA by binding to the 5' UTR of the viral RNA.

Question 254

In which families listed below no expression of viral mRNAs could be detected in any of the examined members? - Herpes viridae - Polyomaviridae - Adenoviridae - Flaviviridae - Poxviridae - Picornaviridae Explain these observations functionally

Answer 254

- Flaviviridae - Poxviridae - Picornaviridae -> no nuclear phase -> miRNAs generated in nucleus

Question 255

What special mechanism does HCMV use for the egress of new formed virus particles from the nucleus of infected cells? Which cellular process mimicked by the virus?

Answer 255

HCMV (human cytomegalovirus) protein UL97 has kinase activity and phosphorylates lamina at the sites where CDK1 would phosphorylate during mitoses: Molecular mimicry of cellular kinase

Question 256

HIV-1 Assembly: a) Which cellular protein complex is critical for budding of HIV? b) Which protein of HIV recruits components of this complex and how is the relevant domain in the viral protein called? Give one example for a recruited cellular protein. c) Which domain in the viral protein is critical for there recruitment? d) How would you prove a critical function for a cellular protein of this complex in HIV budding?

Answer 256

a) Endosomal sorting complex required for transport b) GAG, Late domain, TSG101 c) late domain d) siRNA knockdown of TSG101

Question 257

How are experiments called which are used to reduce the number of members of a pre-existing viral quasi species? Design one of those experiments.

Answer 257

Bottle neck experiments - add neutralizing monoclonal antibody to virus, incubate - add mixture to cell culture

Question 258

By which experimental setup it was shown that there is a massive interaction between vesicular stomatitis virus (VSV) and HeLA cells during viral cell entry? Which class of cellular enzymes were identified as keys players?

Answer 258

Systematic siRNA knockdown of all cellular kinases, "Kinasome"

Question 259

Draw the "typical fusion protein" and indicate the names of the relevant domains.

Answer 259

- receptor binding domain - central coded coil domain - membrane anchor

Question 260

a) For which viruses the terms "antigenic shift" and "antigenic drift" are used? b) Explain the terms "antigenic shift" and "antigenic drift"

Answer 260

a) Segmented negative strand viruses like influenza virus b) Drift: slow, point mutations accumulate over time Shift: reassortment of genome segments, drastic, quick

Question 261

Which of the following statements on the HIV-1 protease (PR) are true? - The PR homonymer contains two times the motive DTG (Asp-Thr-Gly) - PR cleaves at the sequence F/YY-P (Phe/Tyr-Pro) - PR cleaves the viral poly proteins Gag and Gag-Pol - The PR homonymer structure is quite similar to the structures of the acidic proteinases Renin and Pepsin - Viral replication capacity drives the evolution of protease mutants in the presence/absence of drugs - Substrat binding to PR follows a "lock-and-key" principle

Answer 261

- The PR homonymer contains two times the motive DTG (Asp-Thr-Gly) - PR cleaves at the sequence F/YY-P (Phe/Tyr-Pro) - PR cleaves the viral poly proteins Gag and Gag-Pol - The PR homonymer structure is quite similar to the structures of the acidic proteinases Renin and Pepsin - Viral replication capacity drives the evolution of protease mutants in the presence/absence of drugs

Question 262

RIG I a) List the three domains of RIG-I (full names) b) RIG-I detects a PAMP. What does PAMP stand for?

Answer 262

a) - Regulatory domain - Helicase domain - cascade activation and recruitment domain b) pathogen associated molecular pattern

Question 263

1. Tat (transactivator of transcription) 2. Rev (regulator of expression of Virion proteins) 3. Vif (viral infectivity factor) 4. Vpr (viral protein rapid) 5. Vpu (viral protein out) 6. Nef (negative factor/ non evident function) A. Hijacks the cellular Cullin5E3 ubiquitin ligase in order to label APOBEC3G for degradation B. is produced in an early stage of infection and plays a decisive role in the onset of events C. Binds to the cytoplasmic domain of the CD4 receptor and induces ubiquitinylation and degradation of the CD4 receptor D. Can act directly as a toxin inducing cell death via apoptosis in uninfected "bystander" T cells E. Promotes the RanGTP dependent export of mRNA out of the nucleus F. Induces the arrest of proliferating infected cells at the G2/M phase of the cell cycle

Answer 263

1. Tat (transactivator of transcription) : D. Can act directly as a toxin inducing cell death via apoptosis in uninfected "bystander" T cells 2. Rev (regulator of expression of Virion proteins): E. Promotes the RanGTP dependent export of mRNA out of the nucleus 3. Vif (viral infectivity factor): A. Hijacks the cellular Cullin5E3 ubiquitin ligase in order to label APOBEC3G for degradation 4. Vpr (viral protein rapid): F. Induces the arrest of proliferating infected cells at the G2/M phase of the cell cycle 5. Vpu (viral protein out): C. Binds to the cytoplasmic domain of the CD4 receptor and induces ubiquitinylation and degradation of the CD4 receptor 6. Nef (negative factor/ non evident function): B. is produced in an early stage of infection and plays a decisive role in the onset of events

Question 264

Which of the following statements on the HIV-1 reverse transcription and integration processes are true? - VPg (Viral Protein Genome-linked) is the primer molecule in reverse transition of the vRNA into proviral cDNA - Reverse transcription involves in total 2 x strand swapping - RT is an RNA- and DNA-dependent DNA-Polymerase deficient of proofreading mechanisms - Reverse transcription can be inhibited by nucleoside and non-nucleosidic inhibitors - Provirus integration into the hosts Genome is at the cost of a 2-base pair loss in the U5 region of each of the two LTRs - IN (intergase) is a dimer displaying two active sites

Answer 264

- Reverse transcription involves in total 2 x strand swapping - RT is an RNA- and DNA-dependent DNA-Polymerase deficient of proofreading mechanisms - Reverse transcription can be inhibited by nucleoside and non-nucleosidic inhibitors - IN (intergase) is a dimer displaying two active sites

Question 265

Lipoproteins of the outer membrane of E. coli - need cytoplasmic ATP for their transport across the periplasmic space - have their signal sequence processed by the standard signal peptidase - are translocated across the plasma membrane using the SecY-dependent translocase

Answer 265

- need cytoplasmic ATP for their transport across the periplasmic space - are translocated across the plasma membrane using the SecY-dependent translocase

Question 266

Which protein factors are needed to support post translational transport across the bacterial plasma membrane via the SecYEG-Tpe translocate, which main energy source are used for the actual translocation ands which amino acids are enriched in the targeting signal (signal sequence)?

Answer 266

Factors: SecA, SecB (not essential) energy sources: ATP, PMF (not essential) amino acids: hydrophobic (N-terminal signal peptide N-H-C-domain, N-domain is positively charged, the H-domain is hydrophobic, and the C-domain is more polar)

Question 267

Which protein factors are needed to support post translational transport across the bacterial plasma membrane via the SecYEG-Tpe translocate, which main energy source are used for the actual translocation ands which amino acids are enriched in the targeting signal (signal sequence)?

Answer 267

Factors: SecA, SecB (not essential) energy sources: ATP, PMF (not essential) amino acids: hydrophobic (N-terminal signal peptide N-H-C-domain, N-domain is positively charged, the H-domain is hydrophobic, and the C-domain is more polar)

Question 268

The signal sequence which directs a protein to the Tat-pathway - bears a so-called Twin-Arginine-Motive blocking its entry into the SecY-dependent translocate - is glycosylated at its N-temrinus after the transfer - is cleaved during the transfer by a signal peptidase

Answer 268

- bears a so-called Twin-Arginine-Motive blocking its entry into the SecY-dependent translocate

Question 269

Lipidation of proteins which are finally located in the outer leaflet of the outer membrane occurs usually - at the periplasmic side of the plasma membrane - at the cytoplasmic side of the plasma membrane - at the periplasmic side of the outer membrane

Answer 269

- at the periplasmic side of the plasma membrane

Question 270

Typ I secretion (T1SS) - consumes ATP during transport - requires the activity of the SecY-dependent translocate - allows gram-negative bacteria the simultaneous secretion of proteins across inner and outer membrane

Answer 270

- consumes ATP during transport - allows gram-negative bacteria the simultaneous secretion of proteins across inner and outer membrane

Question 271

Name all membranes of plastids of the viridiplantae that have proteins coded in the nucleus. For which of these membranes dies the import from the cytoplasm require the activity of the TIC?

Answer 271

membranes with proteins coded in the nucleus: - outer membrane - inner membrane - thylakoid membrane membranes that require the activity of TIC: - inner membrane

Question 272

Signals targeting soluble proteins to the peroxisomal matrix are located - at the N-terminus - at the C-terminus - in an internal hydrophobic segment

Answer 272

- at the N-terminus - at the C-terminus

Question 273

The transport of proteins into the thylakoid lumen may require components with homology - to the bacterial SRP - to the TAT-pathway - to the YidC

Answer 273

- to the bacterial SRP - to the TAT-pathway - to the YidC

Question 274

The targeting to the TOC complex may include steps that require - GTP - PMF - ATP

Answer 274

- GTP - ATP

Question 275

In order to reach their final destination, proteins of the mitochondrial matrix coded in the nuclear genome have to cross - three membranes - one membrane - two membranes

Answer 275

- two membranes

Question 276

beta-barrel proteins of the outer mitochondrial membrane are integrated into the bilayer - After a brief passage across the inter membrane space - after a passage across the inner membrane and the inter membrane space - directly coming from the cytoplasm

Answer 276

- After a brief passage across the inter membrane space

Question 277

The import of proteins into the matrix of peroxisomes requires - the presence of an ATPase in the matrix - a completely unfolded conformation of the substrate - the presence of ubiquitin

Answer 277

- the presence of ubiquitin

Question 278

During maturation of secretory granules - the volume of the lumen decreases - protein maturation by endoproteases is blocked - the pH of the lumen decreases

Answer 278

- the volume of the lumen decreases - the pH of the lumen decreases

Question 279

During receptor down regulation (e.g. of tyrosine kinases) ear-marked receptors are usually endocytose via - Clathrin-dependent endocytosis - the GEEC pathway - phagocytosis

Answer 279

- Clathrin-dependent endocytosis

Question 280

According to the cisternal-maturation model - a complete back-transport of large unfragmented late (trans) Golgi stacks is mandatory - the transport of soluble proteins is mainly performed via transient tubular connections between the different Golgi stacks - vesicular Transport is only essentially involved in the back-transport of molecules

Answer 280

- vesicular Transport is only essentially involved in the back-transport of molecules

Question 281

Sorting of ear-marked receptors during receptor down regulation into internal vesicles requires - COPII coat proteins - Caveolin - ESCRT proteins

Answer 281

- ESCRT proteins

Question 282

Typical protein modifications occurring in the lumen of the Golgi are - acetylation of amino termini of proteins - O-linked glycosylation - further modification of Asa-linked oligosaccharides

Answer 282

- O-linked glycosylation - further modification of Asa-linked oligosaccharides

Question 283

The Exocyst - is involved in the tethering of vesicles during constitutive secretion - supports the recycling of SNAREs after exocytosis directly - consists of globular proteins

Answer 283

- is involved in the tethering of vesicles during constitutive secretion

Question 284

During receptor down regulation (e.g. tyrosine kinases) receptors are ear-marked via - ubiquitinoylation - neddylation - acetylation

Answer 284

- ubiquitinoylation

Question 285

The Golgi apparatus in the yeast S. cerevisiae 1. has no early or late Golgi compartments 2. has usually no stack-like appearance 3- is exclusively concentrated at the microtubule organizing center (MTOC)

Answer 285

2. has usually no stack-like appearance

Question 286

Name the three principle concepts which explain the exchange of luminal content between compartments of the end/lysosomal system

Answer 286

- maturation - vesicular - kiss-and-run

Question 287

The concept of a kiss-and-run mechanism of exocytosis requires a regular and direct involvement - SNARE-proteins - Clathrin - endosomes

Answer 287

- SNARE proteins

Question 288

During receptor down regulation (e.g. of tyrosine kinases) ear-marked receptors are sorted to internal vesicles at the 1. TGN 2. late endosome 3. lysosome

Answer 288

2. late endosome

Question 289

The KDEL-receptor 1. is a membrane protein 2. recognizes signals at the cytoplasmic domains of ER-membrane proteins 3. supports the retrieval of luminal proteins into the ER

Answer 289

1. is a membrane protein 3. supports the retrieval of luminal proteins into the ER

Question 290

name the major mechanistically difference between the process of microautophagy compared to macroautophagy

Answer 290

Micro: Cargo uptake via membrane invaginations Macro: Cargo uptake via envelopment and sealing, then fusion with lysosome -> residual body

Question 291

Tetanus toxin 1. blocks exocytosis by blocking calcium influx to the cell 2. blocks the loading of synaptic vesicles with neurotransmitters 3. is a protease that cleaves and inactivates SNARE proteins

Answer 291

3. is a protease that cleaves and inactivates SNARE proteins

Question 292

Lipid droplets - are degraded after fusion with peroxisomes - have a core of neutral lipids that is surrounded by a lipid bilayer - are formed at the outer membrane of mitochondria

Answer 292

NONE

Question 293

The asymmetry in the lipid composition of the plasma membrane is caused by - specific transport of lipids from one leaflet of the plasma membrane to the other - the restriction of particular biosynthetic pathways to tone of the leaflets of the Golgi membrane - a very fast degradation of lipids at the extracellular leaflet of the plasma membrane

Answer 293

- specific transport of lipids from one leaflet of the plasma membrane to the other - the restriction of particular biosynthetic pathways to tone of the leaflets of the Golgi membrane

Question 294

The non-ovoid shape of nuclei of neutrophils is - controlled by components of the cytoskeleton - important for their capability to migrate from the blood.stream into the surrounding tissues - a result of the lack of nuclear pores

Answer 294

- controlled by components of the cytoskeleton

Question 295

The fusion of mammalian somatic cells - leads to the formation of syncytial tissues - occurs only under pathological or artificial conditions - depends on SNARE proteins

Answer 295

NONE

Question 296

The lipid transport from the ER to the plasma membrane uses - membrane contact sites between the plasma membrane and the endoplasmatic reticulum - membrane containers (e.g. vesicles) of the secretory pathway - lipid droplets

Answer 296

- membrane contact sites between the plasma membrane and the endoplasmatic reticulum - membrane containers (e.g. vesicles) of the secretory pathway

Question 297

The inheritance of the nucleus during open mitosis - needs as an early step the phosphorylation of crucial components like Lamina or nucleoporins - involves the activity of ESCRT complexes to allow the closure of the nuclear membrane after disassembling of microtubules in a late step - is usually accompanied by a massive synthesis of nucleoporins during anaphase

Answer 297

- needs as an early step the phosphorylation of crucial components like Lamina or nucleoporins

Question 298

In mammalian cells sheet-like ER - has usually a constant luminal distance - is only found as part of the nuclear envelope - is usually an important part of the so-called rough ER

Answer 298

- has usually a constant luminal distance - is usually an important part of the so-called rough ER

Question 299

The constriction observed during fission of chloroplasts in viridiplantae requires - actin cables in the inter membrane space of the plastids - dynamin related proteins assembling to a ring in the cytoplasm - a self-assembling GTPase of bacterial origin at the inner membrane

Answer 299

- dynamin related proteins assembling to a ring in the cytoplasm - a self-assembling GTPase of bacterial origin at the inner membrane

Question 300

Vacuoles of the yeast S.cerevisiae are inherited during cytokinesis - by cleaving them into two equally sized parts - by partially vesicularization followed by a myosin and actin dependent transport of these vesicles into the new forming daughter cell - by completely dissolving them into small pieces which are randomly distributed between mother and daughter cell via diffusion

Answer 300

- by partially vesicularization followed by a myosin and actin dependent transport of these vesicles into the new forming daughter cell

Question 301

During cytokinesis - in metazoan the ESCRT complex usually triggers the plasma membrane fusion as the final step of abscission - the formation of the cleavage furrow is regularly observed in adult tissues of viridiplantae - in metazoan the midbody is usually divided between the two daughter cells

Answer 301

NONE

Question 302

A polyA-tail usually enhances degradation - of cytoplasmic mRNA in the yeast S.cerevisiae - of aberrant pre-tRNA in the nucleus of S.cerevisiae - of mRNA in E.coli

Answer 302

- of aberrant pre-tRNA in the nucleus of S.cerevisiae - of mRNA in E.coli

Question 303

Name two examples of biomolecular condensates involved in RNA metabolism. Where within the cell are they located and in which key process are they involved?

Answer 303

Nucleus: Cajal bodies, spliceosomal RNA-modification Nucleus: Nucleolus, spliceosomal RNA-modification

Question 304

The nonsense mediated decay of mRNA - is activated, when a termination codon is outside of a permitted distance to a marker on the particular mRNA - needs always a cleavage by an endonuclease as starting signal - may use the presence of an Exon joining complex as a marker

Answer 304

- is activated, when a termination codon is outside of a permitted distance to a marker on the particular mRNA

Question 305

tRNA maturation in mammalian nuclei involves - addition of a CCA to the 3' end - processing by RNAseP - base modification

Answer 305

- addition of a CCA to the 3' end - processing by RNAseP - base modification

Question 306

Assign a correct term to the numbers depicted in the schematic drawing representing Hemaglutinin!

Answer 306

1 = signal peptide 2 = silica acid binding 3 = clara cleavage 4 = fusion peptide 5 = 6-helix bundle 6 = membrane anchor

Question 307

HIV1-reverse transcription. Are the following statements true? - Vpg is the primer molecule in reverse transcription of the vRNA into cDNA - A single vRNA strand contains two LTRs, each consisting of a U3-, R- and U5-region - RT is a dimeric protein that harbors only one RNase-H domain - The RNase-H domain of RT is for proof-reading - Reverse transcription can be inhibited by nucleoside and non-nucleosidic inhibitors - Provirus integration into the hosts Genome is at the coast of a dinucleotide loss in the U5 region of each of the two LTRs

Answer 307

- A single vRNA strand contains two LTRs, each consisting of a U3-, R- and U5-region - RT is a dimeric protein that harbors only one RNase-H domain - Reverse transcription can be inhibited by nucleoside and non-nucleosidic inhibitors

Question 308

Ubiquitination of host proteins, evoked by certain viral assessors proteins, is a strategy that certain viruses utilize to, for example, evade the hosts immune system. Which of the following HIV assessors proteins are active in host-protein ubiquitination? - Rev, regulator of expression of Virion proteins - Vpu, viral protein out - Nef, non-evident function - Vif, viral infectivity factor - Tat, trans-activator of transcription - Vpr, viral protein rapid

Answer 308

- Vpu, viral protein out - Vif, viral infectivity factor

Question 309

Virus replication - Lückentext

Answer 309

Dengue virus genome replication occurs in membrane vesicles which are INVAGINATIONS from the ER membrane. Dengue shows more similarity to RUBELLA VIRUS. Newly formed Dengue visions are transported from the ER to the Golgi apparatus. In the TRANS-GOLGI pre-M is cleaved by FURIN. pre REMAINS BOUND TO E due to the ACIDIC pH until the visions are secreted from the cell.

Question 310

Some viruses have always a lipid envelope (LE), others exist in naked as well as pseudo-enveloped form (PE). - Hepatitis C virus - Hepatitis A virus - Hepatitis B virus - Hepatitis E virus

Answer 310

- Hepatitis C virus: LE - Hepatitis A virus: PE - Hepatitis B virus: LE - Hepatitis E virus: PE

Question 311

Some viruses have a very narrow (N), others a very broad (B) spectrum of host species. - Hepatitis C virus - Yellow Fever virus - Hepatitis B virus - Rabies virus

Answer 311

- Hepatitis C virus: N - Yellow Fever virus: B - Hepatitis B virus: N - Rabies virus: B

Question 312

A minority of viruses utilize non-canonical mechanisms in the biogenesis of miRNA molecules. Which of the following statements are true? - Some viral pre-miRNAs are transcribed by RNA polymerase III - All viral miRNA precursors are transcribed by RNA polymerase II - All viral pre-miRNAs are exported into the cytoplasm by exporting 5 - All viral pre-miRNAs are exported into the cytoplasm by exportin-1 (Crm1) - All viral miRNA precursors are processed by drohst - All viral pre-miRNAs are processes by dicer

Answer 312

- Some viral pre-miRNAs are transcribed by RNA polymerase III - All viral pre-miRNAs are exported into the cytoplasm by exporting 5 - All viral pre-miRNAs are processes by dicer