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BICD 110 > Midterm 2 > Flashcards

Midterm 2 Flashcards

1
Q

Pathways of entry into human cells

A
  1. Phagocytosis
  2. Macropinocytosis
  3. Clathrin-dependent endocytosis
  4. Caveolin-dependent endocytosis
  5. Clathrin and caveolin independent pathways
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2
Q

Phagocytosis

A

-engulf >500 nm
-actin dependent
Step 1: detection of opsonized targets
-antibody (Fab antigen binding and Fc binds to Fc receptor)
Step 2: formation of phagocytic cup
Step 3: phagosome maturation
-fusion of early endosomes with early phagosome delivers V-ATPASES, pH decreases
-RAB 5 -> RAB 7, pH decreases more
-fusion of lysosome = degradative enzymes
-NADPH oxidase complex
-after degradation of contents, remainders exocytosis

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3
Q

Macropinocystosis

A

-actin dependent, engulfs fluids, not specific
-200nm - 10 um
-membrane ruffles induced by growth factors

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4
Q

Clathrin-dependent endocytosis

A

-clathrin coated pits -> clathrin coated vesicles
-receptor mediated
-needs dynamin
- AP2 specifically localized to the plasma membrane
1. Coat assembly and cargo selection
2. Bud formation: PIP2 on membrane and cargo binding triggers an open conformation in AP2 = induction of curvature. AP2 binds to hydrophobic motifs on receptor
3. Vesicle formation: clathrin triskelion and dynamin to bud off membrane
4. Uncoating: by Hsc70 and auxilin

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5
Q

What happens after material is endocytosed

A

Primary endosomes mature from early to late endosomes and eventually fuse with lysosomes
-rab 5 -> rab 7
-low pH (7 -> 5) in lysosomes activates degradative enzymes
- V-type ATPases in the lysosomal membrane pump protons into the lumen of lysosomes = lower pH

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6
Q

Receptor mediated endocytosis of low- density lipoprotein (LDL)

A

-cells take up lipids from the blood in the form of lipoprotein complexes
-shell composed of a single apoliprotein and a phospholipid mono layer containing cholesterol
-hydrophobic core
-LDL particle: single molecule apoliprotein (ApoB)
-experiment: uptake of LDL particles labeled with ferritin (FH patient cells cannot endocytose LDL = increase in cholesterol)

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7
Q

Structure of LDL receptor

A

-NPXY sorting signal in cytosolic tail of LDL receptor- B propeller domain - ligand binding arm (R1-R7)
-cys rich hook binds APoB at pH 7
-pH 5 in late endosomes weakens the interaction between hook and LDL = release of LDL

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8
Q

Receptor mediated endocytosis of LDL: mechanism

A
  1. PIP2 + cargo receptors = open conformation of AP2. Binding of LDL receptor to LDL particle at ApoB at pH 7
  2. Vesicle formation
  3. Dynamin buds off vesicle
  4. Hsc 70 and auxilin uncoating vesicle
  5. Early endosome -> late endosome. At pH 5, hook releases LDL
  6. Uptake of cholesterol in lysosome and recycling of LDL receptor to PM
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9
Q

How to degrade cytosolic portions of membrane proteins: multivesicular bodies (MVB)

A
  1. Lysosomal enzymes are targeted from the TGN to the late endosome
  2. Endosomes carrying endocytosed PM receptors fuse with the late endosome
  3. Budding of vesicles containing PM receptor into late endosome (=MVB)
  4. MVBs fuse with lysosome= degrade PM receptor
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10
Q

Formation of MVBs require the ESCRT machinery

A
  1. proteins targeted for degradation are tagged with ubiquitin at the PM, TGN, or endosomal membrane
  2. Hrs sorts ubiquitinylated cargo into inward facing buds
  3. ESCRT bunches bud off
  4. VSP 4 requires ATP hydrolysis to regenerate ESCRT
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11
Q

Authophagy enables cells to degrade intracellular contents

A

-ATG proteins induce formation of cup shaped membrane structure
-ATG 8 forms coat around auto phagosome
1. Envelops contents in 2 bilayers
2. Fusion to lysosome releases a single membrane vesicle into the lysosome

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12
Q

Caveolae are stable PM domains

A
  • caveolin (hair pin high affinity for cholesterol), cholesterol, palmitoylation
    -stable membrane domains that depend on cholesterol
    -can contribute both to exocytic and endocytic events
    -might contribute to mechanosensing, lipid regulation, and signaling
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13
Q

Clathrin and caveolin independent endocytosis

A
  • no coats
    -requires dynamin
    -actin
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14
Q

Special mechanisms of endocytosis in polarized cells

A
  • apical (microvilli structure) and base lateral membranes
    -apical: HIV and influenza A buds off
    • enriched in cholesterol and sphingolipids
      -basolateral: VSV G
      -transcytosis: transfer macromolecules from apical to basolateral and vv
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15
Q

Channels

A

-mvmt of ions/water along their electrochemical gradient
-open in response to chemical or electrical signals
-10 - 100 million ions/sec
10^7 - 10^8

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16
Q

Transporters (3 types)

A
  1. Uniporter: (facilitated transport) of a single type of molecule along its concentration gradient
  2. Symporter and 3. antiporter: (co transport, secondary active transport) energy available from ion down an electrochemical gradient, driving movement of molecule against its concentration gradient

-100-10,000 molecules/sec
10^2 - 10^4

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17
Q

ATP powered pumps (4 classes)

A

-ATP hydrolysis drives movement of specific ions against their electrochemical gradient
-10^0 - 10^3 ions/sec
- K+ and X- inside the cell, everything in the blood
1. P class pumps
2. V class pumps
3. F class pumps
4. ABC superfamily

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18
Q

Cooperativity of membrane transport proteins at the PM

A

-Na+/K+ pump: 3Na out, 2K in
-K+ channel: facilitated transport of K+ ions out
-Na+/ lysine co-transporter symporter: energy from downhill movement of Na into the cell, allowing lysine to go inside the cell (uphill mvmt)

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19
Q

Regulated exocytosis of insulin

A
  1. If blood glucose too high, GLUT2 facilitated transporter transports glucose in the cell
  2. Glucose -> pyruvate increases ATP in cytosolic
  3. ATP binds to and closes ATP sensitive K channels
  4. K efflux causes small depolarization of the PM
  5. Depolarization opens voltage sensitive Ca channels
  6. Ca influx triggers fusion of insulin containing secretory vesicle with the PM = release of insulin
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20
Q

Aquaporins

A

-homotetramer
-hydrophilic amino acids residues
-H bonds and narrow pore diameter prevent passage of ions

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21
Q

Glucose uniporters

A

Vmax depends on number of transporters
Km conc at which the rate of glucose uptake is half maximal (dec Km = inc affinity)

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22
Q
  1. P class pumps
A

-generate ion gradients across membranes
-alpha unit: phosphorylated
-beta subunit: unknown function
-Na+/K+ pump

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23
Q
  1. V class pumps
A

-transport of H+ against a concentration gradient
-generate low pH
-not phosphprylated during proton transport
-hydrolysis of ATP triggers a 120 deg rotation of V1 relative to V0, driving proton translocation from the cytosol (matrix) to the lumen (inter membrane space)
-ATP -> ADP

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24
Q

Acidification additionally requires Cl- channels

A

-Accumulation of H+ and Cl- in the lumen lowers pH
- no more electric potential

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25
Q
  1. F class pumps
A

-transport of H+ from lumen (inter membrane space) to cytosol
- no phosphoprotein intermediate
-ADP -> ATP

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26
Q
  1. ABC superfamily
A

-2 transmembrane domains (T) and 2 cytosolic domains (A)
- ATP -> ADP
-export a wide variety of toxins and drugs from the cell
-ex: ABCB1- in drug resistant cancer cells

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27
Q

CO2 transport in blood requires a Cl-/ HCO3- antiporter (AE1)

A

-CO2 converts to HCO3-to increase solubility= O2 released
-in systemic capillaries, high CO2, low O2
-downhill movement of Cl- into erythrocyte = uphill mvmt of HCO3- out of the cell

-in lung capillaries: low CO2, high O2

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28
Q

Trans cellular transport of glucose from the intestinal lumen into the blood

A
  1. Na/K ATPase maintains concentration gradients. Outward mvmt of K through K channels= inside negative membrane potential
  2. Na conc gradient and membrane potential drive uptake of glucose from intestine by 2 Na/glucose symporter
  3. Glucose transported from cell to blood by basolateral glucose uniporter GLUT2
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29
Q

4 types of extra cellular signaling

A
  1. Endocrine signaling: affect distant target cells; signals transported through the circulatory system (epinephrine, insulin)
  2. Paracrine signaling: nearby target cells (neurotransmitters, growth factors)
  3. Autocrine signaling: respond to signal they secrete (growth factors)
  4. Cell-cell contacts: direct contact with surface receptors of adjacent cell
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30
Q

Signals can be hydrophilic or hydrophobic

A

Hydrophobic signals:
-diffuse across PM
-steroids
-bind to cytosolic receptors
-complex moves into nucleus
-binds promoters in DNA to activate/repress gene expression

Hydrophilic signals:
-bind to cell surface receptors
-receptor activates downstream signaling proteins and second messengers
-activate effector protein

31
Q

General principle of a signal transduction pathway

A
  1. Receptor binds to ligand
  2. conformational change in the receptor. Activated receptor binds to signal transduction protein 1
  3. Amplification: signal transduction protein 1 binds other transduction proteins S2 (activates/inhibits)
  4. S2 activates additional signaling proteins, diff targets/ location inside the cell
  5. Activate effector protein
  6. Feedback loop
32
Q

Signal receptor types: G protein coupled receptors (GPCR)

A
  • 7 transmembrane domains
    -N out, C in
    -orphan receptors: ligands not identified
    -30% of all drugs used in humans are agonists/antagonists of GPCRs
    -family A, family B, family C
    -coupled to trimeric G proteins (a, B, Y)
    -GPCR binds to the alpha subunit of the trimeric G protein; GPCR are GEFS for trimeric G proteins
33
Q

General GPCR signal transduction pathway

A
  1. Ligand binding = receptor activation and conformational change
  2. Activated receptor binds to alpha subunit of trimeric G protein
  3. GPCR GEF activity stimulates G-alpha to release GDP
  4. GTP binds to g alpha and activates it
  5. Beta and gamma subunits of the trimeric G protein dissociates from the alpha
  6. G-alpha- GTP activates effector enzyme
  7. G alpha intrinsic GTPase activity hydrolyzes GTP to GDP (no GAP)
  8. G alpha dissociates from effector enzyme, turning it off
34
Q

Second messengers

A

Effector proteins
Adenylyl cyclase + ATP -> cAMP -> PKA
Guanylyl cyclase + GTP -> cGMP -> PKG
Phospholipase C + PIP2 -> DAG (+Ca) -> PKC
-> IP3 -> opens Ca channels in the ER

35
Q

Hormone induced activation and inhibition of adenylyl cyclase (effector protein)

A

G alpha s (trimeric G protein): stimulates adenylyl cyclase (effector)
G alpha i: inhibits adenylyl cyclase

Starts with stimulatory/inhibitory hormones

36
Q

Camp activates PKA

A

-PKA phosphorylates multiple intracellular target proteins (with ser/thr residues)
-camp activates PKA by releasing inhibitory subunits (-camp inhibits catalytic subunit, +camp releases catalytic subunits)
-4 camp = 2 active PKA

37
Q

PKA controls gene expression through CREB

A

-PKA induces expression of enzymes involved in gluconeogenesis
1. Camp
2. Activates PKA
3. PKA catalytic subunits translocate into the nucleus
4. PKA phosphorylates CREB transcription factor
5. CREB forms complex with co activator CBP/P300, stimulating transcription of genes control by a CRE

38
Q

Phospholipase C (effector protein)

A

-GPCR-G alpha activates phospholipase C
-generates two key second messengers from PIP2 (DAG and IP3)
1. GPCR activates PLC
2. PLC cleaves PIP2 = DAG and IP3
3. IP3 interacts with Ca channel in the ER
4. Ca ions released into cytosol
5. CA binding + DAG activates PKC
6. Activated PKC leaves membrane to phosphorylation sub cellular targets

39
Q

Arrestin inactivates GPCR via endocytosis

A

-prolonged PKA activation = phosphorylation of ser/thr residues on cytosolic domain of GPCR
-GPCR cannot activate G alpha
-phosphorylated receptor binds arrestin
-recruitment of AP2 (clathrin mediated endocytosis)
-some GPCRs are dephosphorylated and recycled to the PM

40
Q

Signal receptor type: receptor tyrosine kinases (RTK)

A

-ligands: soluble or membrane bound peptide or protein hormones (growth factors)
-RTK cytosolic domains contain an intrinsic protein tyrosine kinase catalytic site
- (-)ligand: monomers with poorly active kinases
- (+) ligand: two ligands = RTK homodimerizes, cytosolic domain kinases phosphorylates each other, docking site for SH2 and other and other binding domains

41
Q

RTKs activate the small GTPase Ras via adapter proteins

A
  1. Fibroblast growth factor (FGF) binds to FGF receptors = formation of homodimers = autophosphorylation of the cytosolic domains on tyrosine residues
  2. Phosphotyrosine provides a binding site for the SH2 domain of the adapter protein GRB2
  3. SH3 domain on GRB 2 bind proline domains on SOS
  4. SOS is tethered to the membrane and interacts with Ras-GDP
  5. SOS has GEF activity toward Ras = release of GDP and form active Ras-GTP
  6. Ras-GTP interacts with the autoinhibitory domain on Raf= triggers dephosphorylation of Raf
  7. Raf releases 14-3-3 protein, which was stabilizing its inactive conformation
  8. Ras GTP hydrolysis to Ras-GDP = release active Raf
  9. Raf phosphorylates and activates MEK
  10. MEK phosphoprylates MAP kinase on tyr and ser/thr residues
  11. MAP kinase phosphorylates transcription factors
42
Q

Induction of gene transcription MAP kinase

A
  1. Dimeric MAP kinase phosphorylates p90, p90 moves into nucleus, phosphorylates SRF
  2. MAP kinase move into nucleus directly phosphoprylates TCF
    3.phosphorylated TCF and SRF together simulate the transcription of c-fos and other other genes that contains SRE sequence
43
Q

Membrane less compartments

A

-spherical (surface tension)
-coherent assembly of biological macromolecules
-liquid like
-liquid liquid phase separation (LLPS)
-found in both cytosol and nucleoplasm

44
Q

Proteins have different physical states

A

Gas: soluble molecules
Liquid: membrane less compartments
Solid: pathological aggregates

45
Q

LLPS

A

-thermodynamically driven (higher entropy, lower energy)
-phase diagram for proteins that undergo LLPS:
-open compartments (exchange of molecules between dilute and dense phase)

46
Q

Difference in the behavior of liquids and solids

A

Liquid: short range positional order
Solids: long range positional order

47
Q

Certain proteins are prone to undergo LLPS: Intrinsically disordered proteins (IDP)

A

-IDPs have IDRs (intrinsically disordered regions) that don’t form secondary structures
-occupy more space than folded domains
-Low binding affinity for other IDPs
-ex: sec 16
-300 unique proteins in human undergo LLPS
-about 50% of all proteins in humans have IDRs

48
Q

Certain proteins are prone to undergo LLPS: networks of multivalent scaffolds

A

-Multivalent proteins cluster together high affinity domains
-SH2 domains on GRB2 bind phosphotyrosine residues
-SH3 domains bind polyproline motifs

49
Q

Impact of valency on proteins that undergo LLPS: stickers and spacers model

A

Increase in valency = increase in LLPS

50
Q

Implication of membrane less compartments (SKIB)

A

A) reaction specificity: can increase reaction kinetics and specificities
B) reaction kinetics: changes in the physical properties of membrane less compartments can affect the kinetics of reactions (ex increased viscosity)
C) reaction inhibition by sequestration: sequestering molecules inside condensates can prevent reactions from occurring
D) concentration buffering: as a buffer for molecules in the bulk phase (release/ sequesteration of molecules)

51
Q
A

-Without energy input, condensates harden out
-multiple factors control the material state of a membrane less compartment: PLC
1. Post translational modifications: (ex phosphorylation and methylation) can control the fluidity of condensates
2. Ligands: can be protein or nuclei acid binding partners
3. Changing conditions: (ex pH, temp, salt, ATP conc)

52
Q

Example of a membrane less organelle: stress granules

A

-phase separated, membraneless, cytoplasmic ribonucleoprotein assemblies
-primary function: promote cell survival by condensing translationally stalled mRNAs, ribosomal components, etc

53
Q

Maturation and aging of stress granules

A
  1. Liquid condensate -> mature stress granule
  2. Liquid condensate -> aberrant stress granule (mop up unfolded proteins) -> chaperones (help fold) -> degradation or success

Stop translation bc when stressed, unfolded proteins form

54
Q

Example of a membraneless organelle: synaptic densities

A

-phase separation of synapsid and synaptic vesicles creates the reserve pool in the pre synapse
-condensation of SV tethering proteins with VG Ca channels at the active zone
-post synaptic densities form by PSD-95, CAMs, and NT receptors

55
Q

Nucleoli are membraneless sub compartments of the nucleus

A

-1-5 nucleoli per nucleus
- >500 different proteins
- where rDNA is encoded
-rDNA is transcribed into rRNA
- assemble with r-proteins into mature ribosomes
-phase separated structure
-RNA required for assembly of signal recognition particle is manufactured in the nucleoli as well

56
Q

3 distinct zones in the nucleoli (FDG)

A

FC: transcription of rDNA
DFC: rRNA processing
GC: ribosome assembly, storage for unfolded proteins

57
Q

Nuclear pore complex (NPC)

A

-two bilayers separate the nucleoplasm from cytosol
- NPC spans both membranes
- proteins <40 kDa can diffuse through NPC
- proteins > 40 kDa require nuclear localization or nuclear export signal, nuclear transport receptors, Ran GTPases, Ran GEFS and GAPs
-messenger ribonucleoprotein mRNP are transported by a Ran-independent pathway

58
Q

Nucleoporins

A

-FG- nucleoporins: extended disordered structures that have interspersed hydrophilic regions
-membrane nucleoporins:
-structural nucleoporins: 16 copies of the Y complex
- gel like condensate that allows diffusion of molecules <40 kDa

59
Q

Nuclear localization signals (NLS) direct proteins to the nucleus

A

-don’t have a strict motif but are rich in basic amino acids
- 7 residue NLS: PKKKRKV

60
Q

Nuclear import mechanism

A

In cytoplasm:
1. Importin binds to NLS of a cargo protein, forming an importin-cargo complex
2. Complex diffuses through the NPC

In nucleoplasm:
3. Ran-GDP activated by GEF releases GDP and binds GTP
4. Ran-GTP binds to the importin, causing importin conformational change that releases the NLS cargo protein

System recycling:
5. Importin-RanGTP complex is transported back to the cytoplasm
6. GAP associated with the cytoplasmic filaments of the NPC leads to hydrolysis of RanGTP to ranGDP
7. RanGDP conformational change releases importin

*Localization of GEF in nucleus and GAP in cytoplasm ensures direction of nuclear import

61
Q

Nuclear export mechanism: ran dependent

A

-NES don’t have a strict motif but are rich in hydrophobic amino acids

In nucleoplasm:
1. Exportin 1 binds to form complex with NES-cargo protein and Ran-GTP
2. Complex diffuses through NPC

In cytoplasm:
3. Ran-GAP associated with the NPC cytoplasmic filaments = RanGTP hydrolysis to ranGDP
4. RanGDP conformational change releases NES-containing cargo protein into cytosol

Recycling system:
5. exportin 1 and ranGDP are transported back into nucleus
6. RanGEF in the nucleoplasm converts ranGDP to ranGTP

62
Q

Nuclear export mechanism: ran-independent

A

-for nuclear export of mRNA protein complexes (mRNP)

In nucleus:
1. Heterodimeric NXF1/NXT1 nuclear export receptor complex bind to mRNA protein complexes
2. Complex diffuses through NPC

In cytoplasm:
3. RNA helicase (Dbp5) located on the cytoplasmic side of the NPC uses ATP energy to remove NXF1 and NXT1 from the mRNA

Recycling system:
4. Ran-GDP dependent import recycles free NXF1 and NXT1 back into nucleus

63
Q
A

-a lamina reinforces the inner membrane of the nucleus
-humans have 23 pairs of chromosomes
-karyograms are prepared in mitosis cells when chromosomes are maximally condensed
-interphase nuclear chromatin is organized into distinct, non-overlapping territories

64
Q

Structural organization of chromosomes

A

-each chromosome consists of a single DNA molecule
-organized into increasing levels of compactions from nucleosomes to higher order chromatin by histone and non histone proteins (compaction ratio 1:100,000)
-nucleosome: about 147 bp of DNA wound around an octamer protein core (containing 2 copies each of histones H2A, H2B, H3, H4)
-histone surface has positive charges, holding the negatively charged DNA
-147 bp DNA is wrapped one and 2/3 turns around the histone core
-beads on a string arrangement of nucleosomes in chromatin

65
Q

SMC complex (cohesin) condenses chromatin

A

-SMC complex clamps chromatin strands together
-formed by coiled coil proteins Smc2, Smc4, and Kleisin

66
Q

Post transcriptional modifications (PTM) control compaction of chromatin

A

-chromatin function is controlled by PTMs of histone proteins
-acetylation, methylation, phosphorylation, ubiquitinylation
-methylation compacts chromatin, acetylation opens it
-condensed supcompartments within chromosomal territories: spatial control of chromatin organization via LLPS?

67
Q

Internal structure of mitochondria

A
  1. Outer mitochondrial membrane: pores for passive diffusion of molecules <500kDa
  2. Intermembrane space
  3. Inner mitochondrial membrane
  4. Matrix
68
Q

Targeting of nucleus encoded proteins to mitochondrial matrix

A

-amphipathic N terminal targeting sequences target proteins to the mitochondrial matrix
-N terminal 20-50 amino acids alpha helix
-positively charged and hydrophobic on opposite sides

  1. Precursor proteins synthesized on cytosolic ribosomes are maintained in an unfolded state (bound by chaperones ex Hsp70)
  2. Matrix targeting sequence (MTS) binds to outer membrane import receptor Tom20/22
  3. MTS inserted into outer membrane translocon Tom40
  4. Translocating protein moves through Tom40 and inserted into inner membrane translocon Tim (23/17, 44)
  5. Matrix Hsp70 pulls peptide into matrix. MTS removed by matrix protease
  6. hsp70 ATP hydrolysis releases newly imported protein
  7. Protein folds
69
Q

Targeting of nucleus-coded proteins to the inner mitochondrial membrane

A

Path A) Same route, but once Hsp70 has the sequence in Tim 23/17, it moves it to the inner membrane
Path B) same route, but Hsp70 pulls out the entire sequence (with Oxa1 targeting sequence) into the matrix, then its reinserted into the inner membrane by Oxa1
Path C) same route, but Tom 70 instead of Tom20 in the other membrane. No matrix targeting sequence. Then Tim 9/10 -> Tim 22/54 in the inner membrane = many anchored protein

70
Q

Targeting of nucleus encoded proteins to the intermembrane space

A

Path A) same path, then once in the inner membrane, protease cleaves protein and releases protein in the intermembrane space
Path B) no matrix targeting sequence. Sequence goes through Tom40, then S-S bonds form in the intermembrane space

71
Q

Targeting of proteins to peroxisomes

A
  1. Peroxisomal targeting sequence PTS1 on C terminus of unfolded protein (S-K-L). PTS1 binds to Pex5 receptor
  2. Pex5/PTS1 complex binds Pex14 receptor in peroxisomal membrane
  3. Protein released from Pex5
  4. Ubiquitinylation of Pex5 by Pex2/10/12 complex
  5. ATP dependent removal of Pex5 from the membrane by ATPase proteins Pex1/Pex6
72
Q

Lipid droplets

A

-neutral lipid storage
-biogenesis of lipid droplets
1. TG synthesis within the ER: DGAT (acyltransferase)
2. Formation of an oil lens in the ER membrane
3. Budding and nascent lipid droplet formation = initial lipid droplet
4. Lipid droplet growth and expansion via acquisition of specific proteins
5. ILP -> Formation of ARF1/COP1
6. ILD -> DGAT from the membrane join in the making of the expanding lipid droplet (ELD)

73
Q

Mechanisms for targeting of proteins to lipid droplet surfaces during formation and growth

A
  1. Migration via ER-LD membrane bridge (class 1 proteins)
  2. Targeting from the cytoplasm (class 2 proteins)

BICD 110 (3 decks)

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