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BIOC2301 > Membranes And Cell Signalling > Flashcards

Membranes And Cell Signalling Flashcards

0
Q

How many carbons do cellular membranes usually have?

A

16-20

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1
Q

What does a plasma membrane do?

A

Separates internal/external environment and defines the cell. Provides a functional method for passive/specific uptake of key cellular molecules.

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2
Q

Describe unsaturated, saturated or polyunsaturated cellular membranes?

A

Unsaturated has a double bond, polyunsaturated has multiple double bonds and saturated has no double bonds.

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3
Q

What is cholesterol key to?

A

Fluidity

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4
Q

What are liquid-ordered detergent resistant regions?

A

Regions of cholesterol congregated with sphingolipids which are important for cholesterol transport, endocytosis and signal transduction.

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5
Q

Where do cells store excess lipids?

A

In lipid droplets which are triglyceride and cholesterol rich esters which are formed when lipid levels exceed those required for membrane synthesis in order to store he excess lipids.

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6
Q

What are the three ways membrane proteins associate with membranes?

A

Integral protein, peripheral protein and lipid-liked proteins (aka lipid-anchored).

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7
Q

What are integral proteins?

A

Have single or multiple transmembrane domains which form a permanent attachment and can perform functions inside and outside the cell. Often adapt alpha helical configuration crossing the lipid bilayer.

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8
Q

What are peripheral proteins?

A

Proteins which are attached to the exterior of the lipid bilayer and do not span the membrane. Often the regulatory regions of ion channels and transmembrane receptors.

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9
Q

What are lipid-linked proteins?

A

Usually a N-terminal glycine residue covalently bonded to fatty acyl group (such as palmitate and myristate) which anchors the proteins to either face of the membrane.

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10
Q

What is the fundamental problem to overcome in membrane biosynthesis?

A

Biosynthesis and movement of lipids between organelles.

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11
Q

What are sphingolipids and phospholipids made of?

A

Fatty acids.

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12
Q

What is the role lipid flippases?

A

Move phospholipids from one membrane leaflet to the other.

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13
Q

What are the types of flippases?

A

Energy-dependent, energy-dependent inward, energy-dependent outwards and all are ATP dependent and therefore ATPases.

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14
Q

What are the 3 proposed mechanisms by which lipids are transported?

A

Vesicular transport, transport mediated by small, soluble lipid-transfer proteins and transport mediated by direct contact between membranes.

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15
Q

What can cause differences in lipid composition?

A

Different sites of synthesis.

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16
Q

What are the two major protein sorting pathways?

A

Signal base targeting or vesicle based targeting.

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17
Q

Describe the ER?

A

A large, convoluted organelle which has tubules and flattened sacs whose membrane is continuous with the nucleus and is the site of lipid synthesis and protein assembly. Rough ER is densely studded with ribosomes.

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18
Q

How are proteins targeted to and across the ER using signal based targeting?

A

Co-translational translocation by an N-terminal signal sequence.

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19
Q

Describe the signal sequences used in signal based targeting?

A

Variable, no sequence homology, 16-30 residues in length with 6-12 hydrophobic residues in the center and one or more positive residues at the N-terminus. The signal sequence is cleaved off in the ER lumen by a signal peptidase (but not all signal sequences are cleaved).

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20
Q

What two GTP-hydrolysing proteins initiate co-translational translocation?

A

SRP (signal recognition particle) and translocon.

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21
Q

How does SRP work?

A

Mediated by itself and SRPR. Targets secretory proteins into the ER. Consists of 6 proteins bound to a 300 nucleotide RNA (a ribonucleoprotein). P54 subunit has a hydrophobic cleft which binds to the signal sequence’s hydrophobic region. Hydrolysis of GTP on the SRPR releases SRP and the signal sequence from the receptor.

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22
Q

How does translocon work?

A

After the signal sequence is released from the SRP it binds to the translocon which facilitates insertions of the polypeptide into the ER membrane by forming a channel.

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23
Q

What ensure unidirectional movement across the ER?

A

Sec63 complex/BiP and HSP molecular chaperone located in the ER lumen. Sec63 hydrolyses BiP.ATP causing a conformational change which allows BiP to bind the polypeptide chain. This prevents the polypeptide chain from sliding back and stabilises it so that it can fold properly.

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24
Q

What do integral membrane proteins do?

A

They remain in the membrane.

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25
Q

How many types of integral membranes are there?

A

Five.

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26
Q

What can be deduced from the amino acid sequence?

A

Membrane topology and hydropathy profile which provide important clues about a protein of an unknown function.

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27
Q

Name some post-translational modifications?

A

Sulphation, phosphorylation, hydroxylation, ubiquitination, sumoylation, acylation, glycosylation, disulphide bonds etc.

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28
Q

How many protein coding genes do there appear to be?

A

30000-40000

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29
Q

How many modified proteins are there in the proteins from the 200000 proteins?

A

10 million.

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30
Q

What is N-linked Glycosylation?

A

Attachment of sugar oligosaccharide known as glycan to a nitrogen atom.

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31
Q

How does N-linked Glycosylation link the glycan to the nitrogen atom?

A

Between the saccharide residues in the glycan or linkage between the glycan chain and the protein.

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32
Q

How does Glycosylation act to control peptide formation?

A

Correct Glycosylation allows for folding and transport of protein whereas incorrect can block. Can also protect the protein from degradation and is often required for activity/specificity and intercellular recognition/interaction.

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33
Q

When are disulphide bonds formed?

A

During or soon after translation, formed to stabilise tertiary and quaternary structure, only in the oxidising environment of the ER lumen.

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34
Q

What assists the correct folding of proteins?

A

Chaperone proteins.

35
Q

What proteins are transported out of the ER?

A

Only properly folded/modified proteins.

36
Q

What do improperly folded/modified proteins do?

A

They are taken back through the translocon via retro translocation and degraded in the cytosol by the proteasome. The ERAD pathways targets the proteins for degradation.

37
Q

What happens during oligomer formation?

A

N-linked oligosaccharide chains are added to the luminal portion.

38
Q

What modifications occur in the Golgi?

A

O-linked Glycosylation and proteolytic processing.

39
Q

What is proteolytic processing?

A

The conversion of an inactive or non-functional protein to an active one.

40
Q

When does O-linked Glycosylation occur?

A

In the later stages if protein processing.

41
Q

What modifications occur at the cell surface?

A

Shedding.

42
Q

What is shedding?

A

Proteolytic removal of the extra cellular domains of many membrane proteins generating soluble forms.

43
Q

What are the three types of lipid modifications of cytosolic proteins?

A

Palmitoylation, myristylation and prenylation.

44
Q

What is Lipidation?

A

The addition of hydrophobic molecules to a protein which then attaches it to a membrane.

45
Q

What is palmitoylation?

A

Linked mainly to Cys, often near the C-terminus. It enhances hydrophobicity and membrane association and has a role in trafficking between membrane compartments.

46
Q

What is myristylation?

A

The irreversible addition of a myristoyl group to an alpha-amino group using a covalent amide bond onto a terminal glycine residue.

47
Q

Why is myristylation important?

A

Allows weak protein-protein and protein-lipid interactions, role in membrane targeting and signal transduction, cellular proteins (kinases) and important in HIV infection.

48
Q

What is prenylation?

A

Farnesyl (C15) or geranylgeranyl (C20) attached to cysteine to facilitate attachment to cell membrane.

49
Q

Want can different lipid anchors determine?

A

Subcellular localisation of proteins, Ras proteins, Rab GTPases.

50
Q

What are retention signals?

A

Sequences of amino acids that dictate delivery to organelles.

51
Q

What retention signal retains proteins in the ER?

A

KDEL (main) and KKXX, KXKXX, RKR.

52
Q

What do some proteins do for efficient ER transit?

A

Mask their retention signals.

53
Q

How are proteins imported into the mitochondria?

A

By an amphipathic helix of 20-50 residues with Arginine and Lysine on one side and hydrophobic residues on the other.

54
Q

Name the five types of functions proteins in the inner mitochondrial membrane?

A

Redox reactions, ATP synthase, transport proteins, protein transport machinery and mitochondrial fusion and fission protein.

55
Q

What is required for the import of proteins into the nucleus?

A

Clusters of basic residues.

56
Q

What is required for import into Peroxisomes?

A

SKL at c-terminus

57
Q

What is endocytosis used for?

A

To take up proteins from the cell surface and move them to the interior of the cell and to ingest certain nutrient which is too large to be transported across the membrane via active transport.

58
Q

What type of vesicles does the secretory pathway use?

A

COP 1 and 2 vesicles. COP 2 bud from a translational ER site and go to the Golgi and COP 1 vesicles receive a set of Golgi proteins for retrieval to the ER.

59
Q

What is the trans-golgi network?

A

Used to load proteins into different types of vesicles and dictates delivery of the cargo to be secreted; delivered to the plasma membrane, lysosome, secreted, stored for later secretion etc.

60
Q

How do vesicles bud?

A

Coat polymerization alone is insufficient. Scission of membrane neck required to release transport vesicle - ‘fission’. Highly specialized protein machines recognize, wrap and cut membrane
neck, using free energy of GTP/ATP hydrolysis to drive clipping reaction. Eg. Dynamin - essential family of membrane severing machines.

61
Q

Give the three types of endocytic pathways?

A

Clathrin-mediated, caveolin-mediated and clathrin and caveolin independent internalisation.

62
Q

What is clathrin?

A

A triskelion shaped scaffold protein composed of three heavy and three light chains which polymerises around the cytoplasmic face if the invaginated membrane and act to reinforce it.

63
Q

What are AP complexes?

A

Complexes that connect cargo proteins and lipids to clathrin at vesicles budding sites and bind accessory proteins that regulate coat assembly/disassembly.

64
Q

What do AP1, AP2, AP3 and AP4 do?

A

AP1: for transport between the TGN and endosomes
AP2: for endocytosis
AP3: for protein trafficking to lysosomes and other related organelles
AP4: less well characterised

65
Q

What are the main stages of post-endocytic trafficking?

A

Early endosome, late endosome, lysosome.

66
Q

What are the receptors used in the main stages of post-endocytic trafficking?

A

For early endosome: transferrin receptor (specifically recycling endosomes)
For late endosome/lysosome: LDL receptor
For late endosome/lysosome degradation: Epidermal Growth Factor Receptor.

67
Q

What is macropinocytosis?

A

Involves actin cytoskeleton rearrangements at the plasma membrane, uses macropinosomes formed from the plasma membrane folding back on itself.

68
Q

What is phagocytosis?

A

Only occurs in certain cell types used to take up viruses and larger membrane areas.

69
Q

Where does oxidative phosphorylation take place?

A

In the mitochondria of all eukaryotes.

70
Q

What is Chemiosmosis?

A

The use of a proton gradient from the ETC to synthesise ATP.

71
Q

As the electron transport chain occurs what happens to the redox potential?

A

It becomes more positive.

72
Q

Name complex 1-4?

A

1: NADH-Q oxidoreductase
2: Succinate Q reductase
3: Q-cytochrome c oxidoreductase
4: Cytochrome c oxidase

73
Q

What do reduced flavins do?

A

Act as hydrogen carriers.

74
Q

How do quinones oxidation state differ to flavins?

A

Can still carry protons but can also act as a mobile carrier between complexes as they are lipophilic.

75
Q

Describe how the electrons flow through complex 1 (NADH-Q oxidoreductase)?

A

NADH is oxidised passing electrons to FMN and a number of iron-sulphur clusters to eventually reduce ubiquinone. Also pumps 4 hydrogen ions across the membrane at complex 1.

76
Q

Describe how the electrons flow through complex 2 (Succinate Q reductase)?

A

Succinate is oxidised passing electrons to FAD reducing it and passing the electrons to ubiquinone via iron-sulphur centres.

77
Q

Describe how the electrons flow through complex 3 (Q-cytochrome c oxidoreductase)?

A

One electron gets passed to cytochrome c via a Rieske iron-sulphur centre and cytochrome c1. Pumping two protons across the membrane. The other electron enters the Q cycle and cycles through the two heme groups of cytochrome b. Pumping two protons across the membrane.

78
Q

Describe how electrons flow through complex 4 (Cytochrome c oxidase)?

A

Four electrons are removed from four molecules of cytochrome c and transferred to molecular oxygen via producing two molecules of water. At the same time, four protons are removed from the mitochondrial matrix (although only two are translocated across the membrane), contributing to the proton gradient.

79
Q

What is the P:O ratio?

A

How many molecules of ATP can be made per oxygen atom reduced to water.

80
Q

What is the P:O ratio in vertebrates?

A

3.7 protons per ATP means that P:O is 2.7 for NADH substrates and 1.6 for FADH substrates.

81
Q

What are the 6 steps of photosynthesis?

A

Light harvesting, photochemical charge separation, electron transport, oxidation of electron donor, proton pumping, reduction of electron acceptor.

82
Q

What is chlorophyll a?

A

The principle light harvesting molecule, has a conjugating double bond structure with a central magnesium which is important for excitation and transfer of electrons. Absorbs in the blue and red part of the spectrum and therefore looks green.

83
Q

What happens after an electron has been excited?

A

It either falls back to its ground state and releases heat or light of a longer wavelength or it is transferred to an acceptor molecule, reducing it as it is accepted.

84
Q

What do photosynthetic reaction centres contain?

A

A special pair (where the charge separation occurs), bacteriachlorophyll, bacteriopheophytin, quinone and 4 hemes.

85
Q

Describe the steps to produce a fully reduced quinone?

A

Light energy excites a special pair, an electron moves from the special pair to the bacteriopheophytin, to a quinone molecule. An electron from the cytochrome heme re reduces the special pair and quinone A transfers it’s electrons to quinone B leaving it half reduced. This occurs again and a fully reduced quinone it produced.

BIOC2301 (15 decks)

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