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Membranes practice Flashcards

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1
Q

say the approximate % proteins and % lipids in the following membrane types:

Also say how this affects functional complexity (increases or reduces)

  1. Thylakoid
  2. Inner mitochondrial membrane
  3. Inner membrane of chloroplasts
  4. Outer membrane of mitochondria
  5. Outer membrane of chloroplasts
  6. Plasma membrane of bacteria
  7. Outer membrane of bacteria
A

Reduced protein/lipid ratio –> reduced functional complexity

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2
Q
  1. Label the numbered structures (5P)
A
  1. 1 – Bi-molecular lipid layer
  2. 2 – polar heads of lipid molecules
  3. 3 – non-polar tails of phospholipid molecules
  4. 4 – Carbohydrate of glycocalyx
  5. 5 – Peripheral protein
  6. 6 – glycoprotein
  7. 7 – Integral protein
  8. 8 – glycolipid
  9. 9 – Cholesterol
  10. 10 – Outward facing layer of phospholipids
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3
Q

Name the 3 major classes of membrane lipids

A
  1. Phospholipids
  2. Glycolipids
  3. Sterols
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4
Q

How do sterols affect the physical and chemical properties of phospholipid bilayers?

A
  • Reducing lateral mobility
  • Influencing fluidity and permeability
  • Alter the length of the hydrophobic core
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5
Q

Why haydocarbon chains with kinks lower Tm?

A
  • Kinks in hydrocarbon chains will weaken van-der-waals forces between lipid molecules.
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6
Q

Which Glycerophospholipid dominates in bacteria and is 45% of lipid content in brain and nerves?

A
  • Phosphatidylethanolamine (PE)
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7
Q

Which Glycerophospholipid is:

  • enriched in the brain and retina,
  • low in mitochondiral inner membrane
  • highly enriched in inner leaflet of plasma membrane
  • Serves as a signal for apoptosis
A
  • Phosphatidylserine (PS)
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8
Q

Which glycerophospholipid:

  • is 20% of bacterial membrane
  • is Only major phospholipid in thylakoids of chloroplast
  • is Synthesized in mitochondria and functions as precursor for cardiolipin (in inner mitochondrial membrane).
A
  • Phosphatidylglycerol (PG)
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9
Q

Which glycerophospholipid is:

  • Mostly found in inner mitochondrial membrane of animals and plants – constitutes 20% of total lipid content (also in thylakoids of plants)
  • Also found in cell membrane of most bacteria; archaea contain analog of cardiolipin.
  • Only eukaryotic lipid synthesized in mitochondria (supports endosymbiosis theory)
  • Essential component of several complexes of the respiratory chain
  • Additional roles in apoptosis
  • Based on two DAGs
A
  • Cardiolipin (based on two diacylglycerols (DAGs)
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10
Q

Which Glycerophospholipid is:

  • Major component of Lecithin, isolated from egg yolk
  • 17-40% in plasma membrane of eukaryotes (enriched in ER and tonoplast)
  • Levels decrease in cell as we age
A
  • Phosphatidylcholine (PC)
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11
Q

Which glycerophospholipid is:

  • Minor component on the cytosolic side of eukaryotic cell membranes
  • Can be phosphorylated by various kinases (PIP1, PIP2,PIP3)
  • Important in lipid signaling, cell signaling and membrane trafficking
    • Increases affinity of membranes for peripheral membrane proteins
      • Sorting protein cargo
      • Docking and fusion of transport vesicles
    • –> controls direction of membrane trafficking
A
  • Phosphatidylinositol (PI)
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12
Q

Which sphingolipid is:

  • Found especially in myelin sheath around nerve cell axons
  • Head group is either choline** or **ethanolamine
  • Has a role in apoptosis
A
  • Sphingomyelin
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13
Q

Which sphingolipid is:

  • Important in animal muscle and nerve cell membranes
    *
A
  • Cerebroside
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14
Q

what is Gaucher Disease and which lipid is important with it?

A
  • Cerebroside sphingolipid
  • autosomal recessive inherited disorder:
  • mutation in glucocerebroside (degradation of cerebrosides) lipid builds up in the liver, spleen, bone marrow, and nervous system.
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15
Q

Which sphingolipid is:

  • Found mainly in nervous system
  • Oligosaccharides located on the extracellular surface
  • Negatively charged –> alteration of electrical effects over membrane
  • Participate in cell-cell recognition, adhesion, and signal transduction.
A
  • Ganglioside
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16
Q

which two glyceroglycoplipids are:

  • Most prominent in thylakoid membranes of photosynthetic organisms
  • Conserved from cyanobacteria to plants
  • Ratio is crucial for the stabilization of the membrane bilayer
A
  • Monogalactosyldiaglycerol (MGDG) & Digalactosyldiaglycerol (DGDG)
    • MGDG: Monosaccharide = galactose
    • DGDG: Disaccharide = Diagalactose
    • Most prominent in thylakoid membranes of photosynthetic organisms
    • Conserved from cyanobacteria to plants
    • Ratio of MGDG to DGDG is crucial for the stabilization of the membrane bilayer
      *
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17
Q

How is phosphate released under phosphate limiting conditions?

A
  • Phospholipids are partially replaced by galactolipids under phosphate-limiting conditions.
  • This releases phosphate, allowing it to be used for other essential cellular processes.
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18
Q

Which glyceroglycolipid is:

  • Anionic lipid present in thylakoid membranes (least prevalent)
  • Dispensable under normal growth conditions but important in certain environments, particularly phosphate depleted conditions.
  • Sulfonic acid linkage on the galactose moiety (sulfonic acid is linked to the galactose molecule).
A
  • Sulfoquinovosyl diacylglycerides (SQDG)
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19
Q

Which sterols (or similar molecules) are found in which organisms

A
  • Cholesterol (animals)
  • Ergosterol (yeast)
  • Hopanoid (bacteria)
  • Stigmasterol (plants)
  • Sistosterol (plants)
  • Sterols not found in archaea
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20
Q

Why is Acetyl-CoA suitable to build fatty acids? (reason that this molecule is good for this)

A
  • Fatty acids built by linking C2 moieties.
  • This is the reason that most naturally occurring fatty acids have an even number of carbons.
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21
Q

Synthesis of fatty acid based lipids in animals, yeast and plants

which organelles are different things are synthesized in

A
  • Animals:
    • Mitochondria: Synthesis of cardiolipin
    • Cytosol: Fatty acid biosynthesis (eukaryotes)
    • ER: Fatty acid elongation and lipid synthesis
  • Plants:
    • Mitochondria: Synthesis of cardiolipin
    • Plastid: Malonyl-CoA synthesis and fatty acid synthesis (prkaryotes)
    • Cytosol: Malonyl-CoA synthesis for fatty acid elongation (Eukaryotes)
    • ER: Fatty acid elongation and lipid synthesis
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22
Q

Where in the cell is acetyl-CoA synthesized?

Name 3 Organelles, and draw basic pathway for each

A
  1. Mitochondrion
  2. Plastid
  3. Peroxisome
  4. Cytosol
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23
Q

Name 4 functions of Acetyl-CoA

A
  1. Syntehsis of amino acids, other metabolites
  2. Acetylation of cytoplasmic proteins
  3. Histone Acetylation
  4. Long-Chain fatty acid biosynthesis
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24
Q

How is acetyl-CoA transported to the cytosol from the mitochondria and back?

A
  1. Out of mitochondrion:
    1. Is converted to citrate in mitochondria
    2. transported to cytoplasm
  2. Back to mitochondrion:
    1. Pyruvate is transported into mitochondria
    2. Pyruvate converted to Acetyl-CoA
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25
Q
  • Malonyl-CoA formation - stoichiometric equation and significance of the step
A
  • Acetyl-CoA + HCO3- + ATP –> Malonoyl-CoA + H+ + Pi + ADP
  • This is the first committed step in fatty acid synthesis and it is irreversible.
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26
Q

Acetyl-CoA Carboxylase (ACCase): role and place in system

A
  • Made up of three parts:
    • 1 – Biotin carboxyl carrier protein (co-factor)
    • 2 – Biotin carboxylase
    • 3 – Carboxyltransferase

Process:

  1. Transfer of CO2 to biotin
    1. Catalyzed by the biotin carboxylase
  2. Transfer of carboxyl group (HCO3-) to acetyl-CoA
    1. Catalyzed by the carboxyltransferase
  3. Formation of malonyl-CoA upon transfer of carboxyl group to acetyl-CoA
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27
Q

Biotin (what it is, structure, significance)

A
  • Vitamin B7 (vitamin H)
  • Is a universal motif for the transfer of carbon dioxide – such as in malonyl-CoA formation, where the CO2 is transferred to biotin before being transferred to acetyl-CoA.
  • Also serves as a prosthetic group for many enzymes (carboxylases).
  • Is covalently bound to the ε-amine group of lysine.
  • Two step reaction:
    • ATP-dependent linkage of carbon dioxide onto biotin to form Carboxy-biotin
    • Transfer of activated carboxy group onto the final substrate.
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28
Q

Where do Malonyl-CoA and Fatty acid synthesis take place in Prokaryotes vs. Eukaryotes?

What is the difference between ACCase between them?

A
  • Prokaryotic: Malonyl-CoA synthesis and Fatty acid synthesis take place in Plastid. ACCase location is here.
    • Hetero-ACCase: Smaller ACCase with more subunits (4) – CT is split into α and β subunits
  • Eukaryotic: these processes take place in cytosol. ACCase location is here.
    • Homo-ACCase: Larger ACCase with less subunits (3)
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29
Q

2 ways in which fatty acid synthesis may be regulated

A
  1. rate limiting step = formation of malonyl-CoA
  2. regulation of plastidal ACCase (in prokaryotes)
  3. ACCase inhibition
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30
Q

How may plastidal ACCase be regulated in prokaryotes?

A
  • phosphorylation, feedback-inhibition, Thioredoxin (redox regulation)
  • plants can have different types of ACCases in cytosol and chloroplasts:
    • most monocots and dicots have Homo in cytosol and Hetero in chloroplasts
    • most grasses (Poaceae) have homo in both
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31
Q

How may ACCase be inhibited?

A
  • Aryloxyphenoxypropionates, “fops”, and cyclohexanediones, “dims”
    • Specifically target homo-ACCase (because most grasses only have Homo in chloroplasts)
    • ACCase inhibitors used to control growth of grass weeds in agricultural crop fields
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32
Q

Fatty acid synthesis cycle

A
  1. Condensation (3 possible reactions)
    1. Acetyl-CoA –> Malonyl-CoA
    2. Acetyl-CoA –> Ketobutyryl-ACP
    3. Malonyl-CoA –> Ketobutyryl-ACP
  2. Reduction (2 possible reactions)
    1. Ketobutyryl-ACP –> Hydroxybutyryl-ACP
    2. Butenoyl-ACP –> Butyryl-ACP
  3. Dehydration
    1. Hydroxybutyryl-ACP –> Butenoyl-ACP
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33
Q

what is the key enzyme involved in Fatty acid synthesis cycle?

How is it different between Animals, Yeast, Bacteria, Plants?

A

Fatty Acid Synthase: FAS (purpose and role in Animals, Yeast, Bacteria, and plants)

  • Does all enzymatic activities other than ACCase
  • Animals and yeast: Type I complex – 2 identical subunits, with one peptide chain that catalyzes all consecutive reactions.
  • Bacteria and Plants: Type II complex – several individual subunits (~12 different enzymes). Strict coupling of enzymatic activity.
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34
Q

How is fatty acid synthesis terminated?

What 2 enzymes are involved?

A
  • Thioesterase (hydrolase): hydrolysis of acyl-ACP to free fatty acid
    • Plants have different thioesterases: FatA, FatB, FatC.
      • FatC- specific for short fatty acids
  • Glycerol-3-phosphate acyltransferase: Direct transfer of fatty acid from ACP to glycerol –> lipid
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35
Q

Elongation of fatty acids which enzymes used?

A

elongases

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36
Q

Derivatization of fatty acids

how different in animals and plants

A
  • Mammals: Desaturases
    • Main desaturated fatty acids are 16:1, 18:1, 18:2, and 18:3. It is only possible to desaturate up to position Δ9 in mammals. Some desaturated fatty acids in positions >9 are built by elongation.
    • Localized on cytosolic site of ER-membrane. Desaturases in mammals are phylogenetically related enzymes.
  • Plants: desaturases
    • Contain chloroplast localized, soluble desaturase in addition to ER membrane bound desaturase. Is phylogenetically not related to other desaturases. Contains two irons and is reduced by ferrodoxin. Specifically important for glycerolipids.
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37
Q

How are the lipid backbones of glycerophospholipids synthesized?

A
  • On lipid bilayer of ER, Fatty acids attached to CoA.
  • Glycerol 3-phosphate comes and attaches two fatty acids together with help of an acyl transferase, removing the 2 CoA.
  • Forming glycerophospholipids.
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38
Q

How are the backbones of sphingolipids synthesized?

A
  • Sphingosine = Serine + fatty acid
  • Sphingosine synthesized by condensation of palmitoyl-CoA and serine.
  • The transfer of a second fatty acid to serine creates the sphingolipid/ceramide.
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39
Q

How are phospholipid head groups added in the CDP diacylglyceride pathway?

A
  • CDP Diacylglycerol pathway: Backbone is activated
    • Activation of phosphatidate:
      • Phosphatic acid + CTP à CDP-Diacylglycerol + PPi
    • Transfer of head group
      • CDP-Diacylglycerol + headgroup à Phospholipid + CMP
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40
Q

How are headgroups added in the Diacylglycerol pathway?

A
  • Diacylglycerol pathway: Headgroup is activated
    • Activation of head group
      • Headgroup + CTP à activated headgroup + CMP
    • Transfer of head group
      • Activated headgroup + phosphatidic acid à phospholipid + CMP
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41
Q

How are sphingolipid headgroups added?

A
  • Transfer of headgroup from a phospholipid onto a ceramide
42
Q

How are head groups added in the case of glycolipids?

  • Glycerophospholipids
  • Glycosphingolipids
  • What do Glucosyltransferases do?
A
  • Glyceroglycolipids: attachment of galactose onto diacylglyceride (DAG)
  • Glycosphingolipids: attachment of various saccharides to ceramide
    • Often contain unusual sugars and can be branched.
  • Glucosyltransferases: transfer of activated UDP-glucose
43
Q

Describe cholesterol synthesis in 3 steps

A
  1. Synthesis of isopentenyl pyrophosphate
  2. Condensation to squalene (C3030)
  3. Cyclisation of Squalene
44
Q

Where do the steps of sterol lipid synthesis take place?

A
  • Synthesis of Mevalonate – mevalonate pathway (in the cytosol)
  • Synthesis of farnesyl-PP (in the peroxisome)
  • Squalene synthesis and formation of cholesterol (in the ER)
45
Q

Which enzyme is:

  • Integral protein of the ER membrane.
  • It is a key enzyme of cholesterol synthesis in that it is crucial for mevalonate synthesis.
  • Is tightly regulated via both transcription factors and enzyme activity.
A
  • HMG-CoA reductase
    • Integral protein of the ER membrane. It is a key enzyme of cholesterol synthesis in that it is crucial for mevalonate synthesis. Is tightly regulated via both transcription factors and enzyme activity.
46
Q

Why is proline known as the helix breaker?

A
  • Side chain is jammed into space that should be occupied by backbone
  • a methylene group occupies the position of the hydrogen-bonding amide protein.
47
Q

How many residues per turn in a common TM helix?

A

3.6 residues per turn

48
Q

TM-heli: Right or left handed?

A

Right handed

49
Q

How are the chemical properties of a TM helix determined?

A

Determined by side chains

50
Q

A TM helix typically spans the whole membrane, how thick is it, and how many amino acids in TM helix?

A
  • membrane is ~3.5 - 5 nm thick
  • TM helix is ~15-20 AAs
51
Q

Where are amino acids typically found in the lipid bilayer?

A
  • Aliphatic: found predominantly in core region of bilayer
  • Aromatic: position within the aromatic belt
    • Ring system is perfect for positioning in the polar-apolar interphase of the membrane surface.
    • Why is phenylalanine not found in the aromatic belt? Hydrophobic
52
Q

How are TM-segments formed in the Beta barrel

A

Formed by beta sheets with polar and non polar side chains

53
Q

How does polarity of side chains in beta barrels affect it?

A
  • Results in side chains pointing in opposite directions alternately with regard to the backbone
  • Most porin structures thus consist of alternating polar and non-polar amino acids
  • Polar side chains point towards the hydrophilic inside of the channel
  • Non-polar side chains are in contact with the hydrophobic membrane core
54
Q

What to do if TM-region and lipid bilayer size do not fit? What is this called?

A
  • – Hydrophobic mismatch
    • Lipid bilayer can adjust to the hydrophobic mismatch
      • This is possible because lipid hydrocarbon chains are quite flexible, and can be stretched, squashed and/or tilted.
      • Non-bilayer lipids are often involved in this kind of adjustment
    • The protein can adjust to the hydrophobic mismatch
      • Changes in the tilting angle of the TM-helices can be employed to adjust proteins
55
Q

True or False:

  • The hydrophobic length of integral proteins is normally adapted to the hydrophobic thickness of the membrane span.
A

True

56
Q

How do proteins get into the RIGHT membranes?

A
  • Sorting signals:
    • N-terminal, C-terminal, internal
    • Features of the signal peptides direct the proteins:
      • Positive charge, negative charge, hydrophobic, hydroxylated
57
Q

Hoiw are Signal and tail anchored proteins targeted into the mitochondria mebrane?

A
  • Signal-anchored proteins:
    • N-terminal sorting signal: Hydrophobic stretch, TM-domain
  • Tail-anchored proteins:
    • C-terminal hydrophobic stretch = TM domain
58
Q

How are β-Barrel proteins inserted into mitochondria membrane?

A
  • TOM complex: translocon of the outer mitochondrial membrane
    • β-barrel precursor brought through membrane by TOM
  • SAM (Sorting and assembly machinery)
    • Sorts and assembles β-barrel protein
59
Q

How are inner membrane proteins inserted into the mitochondria?

A
  • Internal signal sequences: Tim22 pathway
  • N-terminal signal sequences – Tim23 pathway
  • Mitochondrial encoded proteins
    • Proteins encoded in matrix of mitochondria
60
Q

How are membrane proteins inserted into the chloroplast outer, inner, and thylakoid membrane?

A
  • Outer membrane
    • β-barrel proteins –> no SAM complex, N-terminal signal sequences.
    • Signal anchored and tail anchored proteins –> similar to mitochondria
  • Inner membrane
    • Stop-transfer sequence or via stroma
  • Thylakoid membrane
    • Insertases:
      • Alb3 mediated insertion into the thylakoid membrane
      • YidC functions as a membrane protein insertase
61
Q

How are proteins inserted into the ER membrane?

A
  • Co-translational translocation
    • Ribosome bound to ER membrane, protein extruded from ribosome into ER
  • Post translational translocation
    • ribosome is free, protein brought to ER
  • Single pass ER transmembrane proteins
    • N-terminal signal sequence
    • Internal signal sequence
  • Double Pass ER transmembrane proteins
    • Start transfer sequence and stop transfer sequence
  • Multi-pass transmembrane proteins:
  • Tail-anchored proteins
    • The GET pathway
  • Phosphatidylinositol anchored proteins
62
Q

how Can lipids flex within monolayer and bilayer?

A
  • Movement within the monolayer: rotation, flexion and lateral diffusion
  • Movement within the bilayer: transversal diffusion (flip-flop)
63
Q

How do lateral and transversal diffusion of lipids within membranes compare in terms of speed?

A
  • Lateral:
    • ~0.1 – 1 um2 per second
    • ~10 – 100 faster than lateral movement of most proteins
  • Transversal: speed varies depending on head group
    • DAG: 10-1 Seconds
    • Cer: 10 min
    • PC: 10 hours
    • LPC >10 Hour
64
Q

Which enzyme has a large role in Glycosylation in ER lumen

A

Flippases

65
Q

Which enzymes are responsible for:

  • Abolishing membrane asymmetry by bi-directional, unregulated transport of lipids
  • Important part of cellular processes such as apoptosis or blood clotting
A
  • Scramblases
    *
66
Q

An experiment is performed

  • Mouse and human cells fused together to created a hybrid cell.
  • Antibodies against mouse membrane proteins and human membrane proteins were introduced.
  • they are labelled with two different colors.
  • At beginning, color is a split down the middle,
  • after incubation the different species membrane proteins are evenly distributed.

What does this experiment demonstrate?

A

Mobility of membrane proteins

67
Q

Experiment:

  • The lipids or protein are marked with a fluorescent dye
  • bleaching of dye by strong laser light
  • wait and see
  • rate of recovery is directly proportional to lipid mobility

What is this experimental technique called, what does it demonstrate?

A

FRAP - Fluorescence recovery after photobleaching

Demonstrates membrane protein mobility

68
Q
  • What is indicated by Time-resolved single-particle tracking?
A
  • In artificial bilayers indicates a movement by simple Brownian motion.
  • Hop diffusion
69
Q

What molecules are:

  • Cholesterol and sphingolipid enriched, highly dynamic submicroscopic (25-100 nm diameter) assemblies. They float in liquid-disordered lipid bilayer in cell membranes.
  • Concentrate and segregate proteins in microdomains
  • Possible role in cellular signaling and trafficking
  • Difficult to analyze in living cells à existence is controversially debated
A

lipid rafts

70
Q

What is an example of fast signaling in lipid transduction?

What is an example of slow signaling?

A

Fast: Muscle contraction

Slow: Cell division

71
Q

Extracellular signaling:

Moleule types:

Process:

A
  • Molecules:
    • Large and/or hydrophilic molecules
    • Cannot pass the plasma membrane of target cells
    • Need receptor molecules at membrane surface
  • Process:
    • Receptor molecules at membrane surface bind to signaling molecule
    • Intracellular signaling components forward the signal to effector proteins
      • Eg. Metabolic enzymes/transcriptional regulators
    • Induction of cellular response reaction
72
Q

Intracellular signaling:

Molecules

Process:

A
  • Molecules:
    • Small and/or hydrophobic molecules
    • Can pass plasma membrane
    • Intracellular binding to receptor/enzyme
  • Intracellular signaling proteins as molecular switches
    • Two central classes:
      • Protein Kinases/phosphatases
      • GTP binding proteins
    • Two important types of protein kinases:
      • Serine/threonine kinases
      • Tyrosine kinases
73
Q

name 3 families of cell surface receptors and an example for each

A
  1. Ion channel coupled receptors
    1. E.g. synapse
  2. GPCRs
    1. CB1 cannabinoid receptor
  3. Enzyme coupled receptors
    1. e.g. Recetor tyrosine kinases (RTKs)
74
Q

Purpose of Cell walls in plants

A
  • Restrict the expansion of the plasma membrane.
  • This results in the so-called cell turgor/turgor pressure.
75
Q

How does the ions and metabolite concentratoin affect cells?

A
  • Cells normally contain a higher inside concentration of ions and metabolites than their environment.
  • This leads to an influx of water to equalize inside and outside osmolarity
    • –> the plasma membrane expands
76
Q

Give an example of voltage dependent ion channels being involved in the signaling process in plants

A

Contact induced shutting of the pinnae of Mimosa pudica

  1. Contact induces a change in membrane potential
  2. Voltage-dependent channels open and release a pulse
  3. Depolarization-induced opening of K+ and Cl= channels
  4. Water loss-induced movement at pulvini (cells at leaf base)
  5. Reversible: H+-ATPase of plasma membrane regenerate membrane potential.
77
Q

Why do stomata open and close in plants?

A
  • Land plants require stomata for gas exchange
    • Regulation of photosynthesis
  • At the same time open stomata are the major cause of water loss.
  • Stomata opening/closing is thus regulated in close correlation to various environmental parameters
78
Q

3 ways in which Membrane ion and metabolite transport may occur

A
  1. Simple diffusion (along conc. gradient)
    1. Hydrophobic molecules and small uncharged molecules (very slow)
  2. Facilitated diffusion (along conc. Grad.)
    1. Down electrochemical gradient with the help of channels and transporters
  3. Active transport (against conc. Grad)
    1. Transport of hydrophilic molecules. Consuming energy with the help of transporters.
79
Q

Why is cellular compartmentalization a prerequisite for energy metabolism in photosynthesis?

A
  • Charge separation across the thylakoid membrane produces electric field
  • Gradient of protons: Proton motive force
  • Synthesis of ATP and NADPH: Assimilatory force
80
Q

Why is cellular compartmentalization a prerequisite for energy metabolism in Respiration?

A
  • Charge separation across the inner mitochondrial membrane
  • Gradient of protons: Proton Motive Force (pmf)
  • Synthesis of ATP: Assimilatory Power
81
Q

Name 5 processes where membrane compartmentalization is used in energy metabolism:

A
  1. Photosynthesis
  2. Respiration
  3. Proton motive force
  4. ATP synthase
  5. Electrochemical gradient across inner mitochondrial membrane
82
Q

3 mechanisms of active transport

A
  1. Coupled transport
  2. ATP-driven transport
  3. Light driven transport
83
Q

When is differential centrifugation helpful?

A
  • Have particles of different size to seperate
  • They will have different sedimentation rates
84
Q

What is Isopycnic centrifugation used for?

A
  • Isopycnic Centrifugation
    • Density gradient centrifugation
    • Separation of particles with different density (and similar size)
85
Q

Describe process of cell disruption from cell or tissue to cell homogenate

4 possible methods

A
  1. Sonification
  2. mild detergence
  3. french press
  4. potter
86
Q

Experiment performed

  • 2 half cells filled with electrolytes
  • Electric circuit with voltage sources and ampere meter
  • 2 Ag/AgCl electrodes
  • Bilayer (with integrated channel)
    • The channel is the only possible electrical connection between the two half cells
    • Only active channels close the electrical circuit
  • Uses the Nernst-equation to correlate membrane potential to the ion gradient

What is this process, what is it studying

A

Process: electrophysiology

Studying: Membrane proteins in their “natural environment”

87
Q

Describe the Patch clamp technique

A
  • Allows the measurement of ion currents in living cells
  • Measures the sum total of single currents caused by all channels within a certain area
  • Depending on the application, the method can also measure single channels
88
Q

How might one Extract lipids prior to analysis

A
  • Incubation of sample with chloroform/methanol denatures proteins
  • Most lipids can be recovered in the chloroform phase
  • Further analysis after evaporation of chloroform and recovery in appropriate solvent
89
Q

4 methods lipid seperation

A
  • Thin layer chromatography
    • 2D thin layer chromatography can separate many lipids by using different solvents for each dimension
  • Adsorption chromatography
  • Size exclusion chromatography
  • Hydrophobicity chromatography
90
Q

Mass Spectrometry - What may be determined by it?

A

Can be used to identify individual atoms and molecules within a sample

How it works

  • Ionization
  • TOF (basic principle)
    • Application of an electrostatic field in the source accelerates ions/fragments: acceleration voltage
    • Ions are separated by their m/z – ratio with a drift distance
    • Differences in m/z – ratios cause differences in velocity
    • m/z ratio can be determined from acceleration voltage and drift distance
  • Quadrupoles
    • Basic principle:
      • 4 metal electrodes arranged in parallel
      • Application of a combined direct/alternating current voltage à AC/DC principle
  • Ion detection
91
Q

What purpose do Chaperones serve in protein transport?

A
  • Prevent folding
  • Maintain protein in an unfolded, translocation-competent form
  • Act as molecular ratchets and provide directionality
92
Q

What purpose does glycosylation serve?

A
  • >50% of eukaryotic membrane proteins, which are processed in the ER, are predicted to be glycosylated
  • Marks progression of protein folding in ER to Golgi transport
  • Resistance to proteolytic cleavage
  • Protection against pathogens
  • Cell-cell recognition
93
Q

What is vesicle transport important for?

A
  • Secretion of proteins/substances
  • Also important for uptake of substances into the cell
  • Remodeling of organelles
94
Q

Which coat proteins are used in different pathways of vesicle transport?

  1. ____
    1. ER to golgi
    2. Retrograde
    3. intra-golgi
  2. ____
    1. ER–>Golgi
  3. ____
    1. Post Golgi
    2. Golgi –> trans-Golgi network and plasmamembrane
    3. Endocytosis
A
  • COPI:
    • ER to golgi
    • Retrograde
    • intra-golgi
  • COPII:
    • ER–>Golgi
  • AP 1-4 + Clathrin:
    • Post Golgi
    • Golgi –> trans-Golgi network and plasmamembrane
    • Endocytosis
95
Q

Purpose of coat proteins in vesicle transport?

A

Select cargo and induce membrane curvature

96
Q

Cholesterols role in receptor mediated endocytosis

A
  • Receptor mediated endocytosis: example cholesterol
    • Cholesterol (LDL) is taken up from the blood by receptor mediated endocystosis
    • Receptors are recycled by retrograde transport
97
Q

Role of GTPases during vesicle formation

A
  • Small GTPases catalyze coat assembly
    • COPII – Sar1p
    • COPI – ARF1
    • Clathin – ARF6
98
Q

Name the 5 steps of vesicle transport

A
  1. Loading
  2. Budding
  3. Movement
  4. Tethering/docking
  5. Fusion
99
Q

How is vesicle transport mediated along actin filaments?

A

transport along actin filaments is assisted by myosin

100
Q

How is vesicle transport mediated along the microtubules

A

Transport along microtubules is mediated by kinesin-dynein

  • Dynein: transports proteins from the periphery of the cell to the center
  • Kinesin: transports to the periphery of the cell
101
Q

How is it ensured that proteins are fusing with the correct acceptor membrane during Vesicle tethering?

A
  • Protein complexes ensure that proteins are fusing with the correct acceptor membrane
    • Rab proteins (monomeric GTPases), Rab effectors, SNARE proteins, SNARE regulators
102
Q

What do SNARE complexes participate in, and what is their structure like?

A
  • Participate in mediated vesicle fusion
  • Structure
    • Chemically very stable
    • Have α-helical coil-coil domains
    • Are resistant against SDS and proteolytic cleavage
    • Dissociation occurs only at 80-90 °C or by specific facts and energy (ATP)

Cell Bio Exam (17 decks)

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