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MOL 348 > Features of the Cell Membrane and Trafficking > Flashcards

Features of the Cell Membrane and Trafficking Flashcards

1
Q

Metacognition

A

Thinking about thinking

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2
Q

Cytoplasm

A

Everything within cell outside nucleus including organelles and cytosol

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3
Q

Cytosol

A

Gel like substance composed of mostly water, ions, and proteins. pH is ~7.4. High concentrations of glutathione which acts as redox buffer.

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4
Q

Cell/Plasma/Cytoplasmic Membrane

A

Membrane made of pure phospholipids is semi-permeable. Constructed from amphiphilic lipids (fatty acids, oils, steroids-water insoluble).

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5
Q

Phospholipid

A

Hydrophobic tails(kink in one to allow for cylindrical shape). Hydrophobic head with Glycerol/sphingosine base, phosphate, and variable top regions.

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6
Q

Passive Transport

A

Requires no energy. Channel-mediated, transporter-mediated, or simple diffusion.

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7
Q

Lipid Bilayer

A

Phospholipids pack together in energetically favorable form (Hydrophobic interior and hydrophilic exterior).
Passes Through Fast: Non-polar (Fat-soluble live estrogen), gases(like O2 or CO2)
Passes Through Slow: Small Uncharged Polar (like water sometimes, ethanol, glycerol, acetic acid at pH 1.5)
Doesn’t Pass Through: Large, polar, charged (like ions, sucrose, acetic acid at pH 10)

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8
Q

Passive Transport

A

Requires no energy. Channel-mediated, transporter-mediated, or simple diffusion. Utilizes concentration gradient with no membrane potential or electrochemical gradient with membrane potential.

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9
Q

Active Transport

A

Requires Energy. Works against electrochemical or concentration gradients.

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10
Q

Diffusion

A

Passively right through the membrane. Diffusion is the net movement of anything from a region of higher concentration to a region of lower concentration. Diffusion is driven by a gradient in concentration.

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11
Q

FRAP

A

Fluorescence recovery after photobleaching . Bleach and see how long it takes to recover light. Quantify lateral diffusion.

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12
Q

Signal Hypotheis

A

Proposes that proteins encore sorting motifs. Proteins that leave the cytosol have intrinsic signals that direct them to the appropriate organelle.

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13
Q

Sorting Signal

A

Coded by protein itself, cis-acting (within/part of the protein). Recognized by Sorting Receptor (trans-acting: something else that can recognize signal) like Signal Recognition Particle (SRP) which recognizes signal as it emerges from ribosome. Binding causes a quick pause in translation. Translation directed to ER. Import Mechanism also involved.

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14
Q

Necessary

A

A necessary condition is a condition that must be present for an event to occur. Can protein do it with or without it?

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15
Q

Sufficient

A

A sufficient condition is a condition or set of conditions that will produce the event. Is protein enough to cause it to happen?

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16
Q

Karyopherins (KAPS)

A

Major Family of nuclear import and export receptors. Similar but different specificities for NLS & NES.

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17
Q

Importins

A

A type of karyopherin that transports protein molecules into the nucleus by binding to NLS. It docks at NPC, moves through, and releases cargo when interacting RanGTP and recycles receptor.

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18
Q

Exportins

A

Exportins bind to proteins with NES in association with ranGTP and dock at NPC. Then it passes into the cytoplasm through the NPC. The protein cargo is released when the GTP is hydrolysed and the exportins diffuse back into the nucleus.NTF2 Mediates nuclear import of Ran.

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19
Q

Nuclear Localization Signal (NLS)

A

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport. Typically, this signal consists of one or more short sequences of positively charged lysines or arginines exposed on the protein surface.

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20
Q

Nuclear Export Sequence (NES)

A

A nuclear export signal (NES) is a short target peptide containing 4 hydrophobic residues in a protein that targets it for export from the cell nucleus to the cytoplasm through the nuclear pore complex using nuclear transport.

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21
Q

Gated Transport

A

Gated transport is most notable as the protein traffic between the cytosol and nucleus occurs between topologically equivalent spaces, which are in continuity through the nuclear pore complexes. The nuclear pore complexes function as selective gates, where selected macromolecules are actively transported while smaller molecules are allowed free passage.

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22
Q

Nuclear Pore Complex (NPC)

A

Have conserved structure with 8-fold symmetry. Composed of NPC proteins (nucleoporins). Have nucleoplamic face “baskets” and cytoplasmic face “filaments”.

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23
Q

Inner Nuclear Membrane

A

Lipid and protein compositions differ with outer membrane. Lamins for the nuclear lamina inside.

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24
Q

Outer Nuclear Membrane

A

The outer nuclear membrane is continuous with the endoplasmic reticulum membrane and internuclear membrane.

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25
Q

Perinuclear Space

A

The space between the nuclear membranes

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26
Q

Small GTPases/Small GTP Binding Proteins

A

Used to witch trafficking signal on and off. GDI=GDP dissociation inhibitor. GDI binds smallGTPase-GDP form and brings it away from lipid bilayer.

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27
Q

GTPase Activating Protein (GAP)

A

Promotes the conversion of GTP to GDP by increasing small GTPase activity .

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28
Q

GTP Exchange Factor (GEF)

A

Exchanges GDP for GTP.

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29
Q

RAN

A

Nuclear import and export. RanGTP enriched in nucleus and RanGDP enriched in cytoplasm. Gives directionality to transport.

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30
Q

Immunofluorescence

A

See protein of interest. Label multiple proteins with multiple colors. You can live image! May interfere with normal function because large! Not always easy to tag with fluorescence.Add antibodies that are fluorescently labeled. Kills cells. Use multiple antibodies to amplify. Also because it’s hard to have Fluorescein specific for an antibody.

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31
Q

Green Fluorescent Protein (GFP)

A

Very bulky. Can use to tag proteins and view live. Make proteins easily visible.

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32
Q

Signal Sequence

A

Usually refers to ER signal sequence. It is hydrophobic. The signal sequence at N-terminal of protein is recognized by SRP as it emerges from ribosome. It is later cleaved off by Signal Peptidase. It then laterally diffuses out of the Sec61 channel and is later degraded.

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33
Q

Translocation

A

Protein is inserted into ER.

34
Q

Conformation Change

A

Change in the shape of a macromoleculed

35
Q

Secretory Pathway/Exocytosis

A

ER->Golgi ->Secretory Vesicles->Destination (Plasma Membrane)

36
Q

Endoplasmic Reticulum

A

Gateway to secretory pathway. Smooth and Rough. Also the storage site of calcium(Sarcoplasmic reticulum)

37
Q

Rough ER

A

Protein translocation to create properly folded luminal and transmembrane proteins and glycoproteins

38
Q

Smooth ER

A

Site of lipid synthesis and membrane biogenesis

39
Q

Co-translational translocation

A

Translation occurs as it is inserted into the ER.

40
Q

Signal Recognition Particle (SRP)

A

Recognizes and binds signal sequence and brings protein/ribosome complex to Sec61 translocon.

41
Q

SRP Receptor

A

In rough ER and binds to SRP so that ribosome can then translocate protein.

42
Q

Sec61 Complex/Translocon

A

Water filled pore. It stays open because proteins bind, changing the conformation and the insertion of hydrophobic signal sequence. Associates with ribosome and serves as entry for protein.

43
Q

Signal Peptidase

A

Cleaves Signal sequence so that it may laterally diffuse.

44
Q

Post-translational Translocation

A

Requires BiP and ATP. Can happen but needs different proteins. Translation on free-ribosome.

45
Q

BiP

A

Chaperone protein that binds unfolded proteins as they are translocated into ER. They protect proteins when they are in the process of folding, shielding them from other proteins that might bind and hinder the process. Post-translational insertion requires BiP and ATP.

46
Q

Chaperone

A

Proteins that help with correct folding

47
Q

Luminal

A

Luminal or Extracellular space (Inside organelles/outside cell)

48
Q

Signal-Pass Transmembrane Protein

A

Need about 20 amino acids to pass through membrane in a simple alpha helix. Can have a signal sequence(a start-transfer sequence) or an internal signal sequence)

49
Q

Multi-Pass Transmembrane Protein

A

Goes through multiple times. Multiple start/stop transfer sequences.

50
Q

Start-Transfer Sequence

A

Hydrophobic sequences.

51
Q

Stop-Transfer Sequence

A

Hydrophobic sequence and becomes transmembrane domain of protein.

52
Q

Hydropathy Plot/Hydropathy Index

A

Plus means hydrophobic (transmembrane region). Must be at least 20 amino acids in length. Count peaks!

53
Q

Positive Inside Rule

A

Cytosol is negative (phosphotidyl-serines). ER Lumen is positive.

54
Q

Topology/Topological Signals

A

Different topologies produced by signal-sequences, anchors, modifications, glycosylated

55
Q

Protein Disulfide Isomerase (PDI)

A

Catalyzes sulfide bonds to form between cysteine in proteins in ER. Assist with folding in ER especially.

56
Q

Glycosyltransferase

A

Enzymes that catalyze the addition of sugar to protein in ER especially.

57
Q

N-linked Glycosylation

A

Occurs in ER. Oligosaccharide added to asparagine (ASN)

58
Q

GPI-Link

A

Lipid anchor added in the ER to protein to keep protein bound to membrane. Temporary C-terminal stop-transfer sequence holds protein until GPI-link is formed

59
Q

Unfolded Protein Response (UPR)

A

Feedback Mechanism to help cope with misfolded proteins. Stimulated by unfolded proteins. IRE1, PERK, and ATF6

60
Q

IRE-1

A

Misfolded proeins activate kinase, self-phosphorilation and dimerization. Endoribonuclease activity is activated and removes intron sin RNA that leads to transcription regulator or ER chaperones that then help fold proteins.

61
Q

Endocytosis

A

Substances are brought into the cell. Includes pinocytosis and phagocytosis. Recycle receptors, nutrients, glucose, viruses, neurotransmitters.

62
Q

Exocytosis/Secretion

A

Cell transports molecules out of the cell by secreting them through pathway. Growth factors, immunoglobulins, hormones, waste, neurotransmitters.

63
Q

Golgi

A

It acts to process and package the macromolecules such as proteins and lipids that are synthesized by the cell. Tubular-vesicular network with cis Face (Close to ER and nucleus) and trans Face (close to plasma membrane). It has distinct sub domains with their own chemicals that modify proteins they see. Extensive remodeling of glycosylation motifs occur in Golgi.

64
Q

Early Endosome

A

Come right from membrane endocytosis. Will mature or recycle. Multiple come together to form multi-vesicular body (a type of late endosome).

65
Q

Recycling Endosome

A

Recycle to plasma membrane instead of being degraded.

66
Q

Late Endosome

A

Will fuse with lysosome to form endolysosome to be degraded .

67
Q

Lysosome

A

Containing degradative enzymes enclosed in a membrane. Can fuse with endosome to form endolysosome.

68
Q

Vesicle

A

Proteins move from place to place via membrane-enclosed transport vesicles.

69
Q

Arf

A

Arf GTPases initiate COP1 and clathrin coat formation at Golgi (Comparable to Sar-1).

70
Q

Sec23/24

A

SAR1-GTP recruits Sec23 which binds to Sar1GTP and then recruits Sec24. Sec24 binds to receptors that recognize cargo and recruit Sec13/31.

71
Q

COPII

A

Involved in transport between ER to Golgi.

72
Q

Dynamin

A

Mediates vesicle scission for clathrin coated vesicles. Forms a helix structure around and GTPase domain of dynamic uses GTP hydrolysis to change conformation.

73
Q

T-SNARE

A

On membrane. Fuse and lock with V-SNARE during docking so that vesicle can fuse. Membranes must be within 1.5nm of each other.

74
Q

V-SNARE

A

On vesicle. Fuse and lock with T-SNARE during docking so that vesicle can fuse.Membranes must be within 1.5nm of each other.

75
Q

Rabs

A

RabGTPases guide vesicles to targets and mediate steps in vesicle transport. Interact with Rab effector protein during tethering. GDI (G-protein dissociation inhibitor) binds RabGDP and keeps it away from membrane.

76
Q

NSF

A

Uses ATP and accessory proteins to unwind SNARES .

77
Q

V-SNARE

A

On vesicle. Fuse and lock with T-SNARE during docking so that vesicle can fuse. Membranes must be within 1.5nm of each other.

78
Q

EndoH

A

EndoH resistance marks entrance into medial Golgi. Early in Golgi, endow can remove sugars, later on it can’t.

79
Q

Pulse Chase

A

Label proteins with radioactivity and then add unlabeled amino acids after to track proteins through secretory process.

80
Q

KDEL

A

a sorting signal for retrieval to the ER. Other signals include KKXX.

81
Q

KDEL-Receptor

A

If it recognizes by KDEL signal, will bud off and be sent back.

82
Q

AP2

A

Clathrin adaptor protein that recognizes endocytic motifs on cargo proteins. Recruits clathrin to come form vesicle. Works on the cell membrane to internalize cargo in clathrin-mediated endocytosis.

MOL 348 (6 decks)

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