Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

MCB > 4-Cell Biology > Flashcards

4-Cell Biology Flashcards

(178 cards)

Start Studying
1
Q

Sub-cellular Organelles

A
  • Nucleus
  • Nucleoskeleton & Lamina
  • Nucleolus
  • ER
  • Golgi
  • Mitochondria
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Nucleus Structure

A
  • Inner nuclear membrane defining the nucleus itself
  • Outer is continuous with ER
  • Membranes fuse at Nuclear pores
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Nucleoskeleton & Lamina

A
  • Consists of Intermediate filaments
  • Nuclear lamina is scaffold-like and surround periphery
  • Made of Intermediate filament-proteins like Lamin A/B/C forming complex meshwork
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Nucleolus structure

A
  • Not membrane bound
  • Liquid-liquid phase separation like a dense droplet inside the nucleus
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What happens in Nucleolus

A
  • Ribosomal RNA synthesis & processing (rRNA)
  • Ribosome assembly
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Rough ER functions

A
  • Orientation of TM proteins
  • Folding proteins (chaperones)
  • N-glycosylation (folding, sorting, stability, hydrophilic making)
  • Co-translational TM-transport of proteins synthed. on membrane-bound ribosomes
  • Transport of unfolded proteins into cytosol for degradation (proteosome)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Smooth ER functions

A
  • Lacks ribosomes (smooth)
  • FA, Phospholipid, & steroid synth.
  • Ca2+ Storage
  • Glucose metabolism (G6Pase)
  • Detoxification (liver)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Golgi Complex (+faces)

A

Flattened membranous sacs = Cisternae for processing, sorting & modification of proteins synthed. on ER
- Cis-face: Nearest nucleus, receives from ER via T.vesicles
- Trans-face: Nearest PM, packages molecules, transporting out of Golgi

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Golgi functions

A
  • O-glycosylation
  • Proteoglycan synth.
  • Lipid mod. (glycolip, sphingomyel.)
  • Proteolysis
  • Sorting (what goes where)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Mitochondria

A
  • Inner membrane makes folds called Cristae
  • Matrix fills inside with ribosomes & DNA
  • CytC store activates Caspases (apoptosis)
  • Brown adipose for heat using ETC
  • Ca2+ storage
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Cytoskeleton Functions

A
  • Provides cell structure & shape
  • Direct intracellular movement
  • Scaffold proteins in metabolism & signal transduction
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Components of Cytoskeleton

A
  • Actin Filaments
  • Microtubules (aB-tubulin dimers)
  • Intermediate Filaments (various)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Cytoskeletal construction & steps

A
  • Polymers held together by weak non covalent interactions
    1) Nucleation, lag phase (rate limiting)
    2) Elongation
    3) Steady state
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Actin (microfilaments) functions

A

Actomyosin complex (moving organelles, muscle, cell division)
- Cell adhesion structures
- Maintenance of cell volume
- Cell cortex (actin network below plasma lamellipodia/fillipodia)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Actin structure & ends

A
  • 7-9nm diameter
  • Made up of monomer globular protein G-actin (ATP for polym.)
  • Has + & - end and polymerizes and is called F-actin (a-helix)
  • Polymer has polarity due to +/- ends
  • Minus end: pointed end, grows slower (ADP bound)
  • Plus end: blunt end, grows faster (ATP bound)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

ARP-complex (actin related protein)

A
  • Responsible for Actin Branching
  • Helps Nucleation (1st step)
  • Has same surface as + end of G-actin
  • ARP form a seed/nucleus for actins to stack on top & branch
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Capping Proteins

A

Binds both ends of Actin filament stabilizing it by preventing assembly/disassembly & is reversible
(make up Z-lines of sarcomere)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Actin fibril regulators

A

When G-actin disassembles its found in a ADP-bound form
- Profilin: ADP to ATP making it ready to bind + end (recharged)
- Thymosin: Binds ATP-bound G-actin, inhibits fibril formation
- Cofilin: Increases dissociation weakening the interactions between ADP-bound G-actin so - end disassembles rapidly

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Actin network/bundles

A
  • Contractile bundle: antiparallel
  • Tight parallel bundle: filopodium
  • Gel-like Network: cell cortex, crisscross
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Actin Bundling Proteins

A
  • Fimbrin: Packs actin closely preventing binding of other proteins
  • a-Actinin: Cross-links loose bundles allowing binding of Myosin
  • Filamin: Formation of loose/viscous gel by binding filaments at angles
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Actin Contractile bundle Regulation

A

a-Actinin
Large protein sits between actin bundles keeping spaces to allow motor protein inside (myosin)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Actin Parallel bundle Regulation

A

Fimbrin
Small protein so less space between fibrils preventing myosin from entering

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Filamin

A

Forms dimers that have 2 legs binding Actin filaments and stabilize cross network formation
- In cell cortex below PM
- Legs have an angle so regulate the angle of the filaments

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What can cut up Actin (severing proteins)

A
  • Gelsolin: Cleaves long actin filaments to shorter ones
  • Cofilin: creats tighter twists so ADP-actin interaction weakens & breaks
    (regulated by Ca2+)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Cytoskeleton during Platelet activation
1) Actin resting is bound by capping proteins, the Ca signal 2) Gelsolin chops actin fibrils 3) Actin filaments grow 4) Filamin, Fimbrin, a-Actinin bind allowing attachment & functions
26
Focal Adhesion & ECM
Integrin receptors on cell surface bind ECM matrix (fibroactin/collagen) and internal cell proteins called Focal Adhesion Complex which connects to Actin network. FAK: Focal adhesion kinase regulates cell growth & if its bound to ECM or not
27
Microtubules
- 25nm diameter - Thickest cytoskeletal element - Grows out from Centrosome - Positions organelles - Moves organelles & vesicles (NT) - Forms mitotic spindle - Moves cilia & flagella
28
Microtubule Structure
- Formed by Heterodimers of a-tubulin (-) & B-tubulin (+ end) - Both bind GTP, only B-tubulin has GTP hydrolysis - Heterodimers form Polymer called Protofilament - Protofilament forms microtubules which are tubes with a lumen
29
Microtubule Nucleation
- Microtubules originate from Centrosome (MTOC) - Centrosome has y-Tubulin serving as platform for a/B-Tubulin to dimerize - Negative end fixed to Centrosome, and + grows
30
Microtubules Dynamic Stability
- B-Tubulin is in a GTP-bound form & allows elongation to Protofilament - GTP hydrolysis happens at + end unless GTP-cap is present - If GDP is on + end, it becomes unstable and shrinks
31
Microtubule end binding proteins
- MAP: Stabilizes growing microtubules for longer & less dynamic mt (neurons) - Catastrophe Factor (kinesin 13): Helps disassembly of microtubules for shorter, more dynamic mt
32
Mitotic spindle types
- Kinetochore MT: to centromere of chromosome (kinesin) - Interpolar MT: bind together & push 2 mitotic spindle poles away (kinesin) - Astral MT: Anchor spindle poles to membrane (dyenin)
33
Intermediate filaments
- 10nm diameter - Prominent in cells with mechanical stress - Nuclear Lamina, Cell shape, Anchoring of Organelles
34
Intermediate filament Structure
No polarity 1) Monomer is protein with a-helical region (rod-domain) 2) Coiled-coil dimer 3) Staggered Tetramer of 2 antiparallel dimers 4) 2 Tetramers packed laterally 5) 8 Tetramers twisted = Rope-like filament
35
Intermediate filament Regulation
- Phosphorylation: Disassembly - Dephosphorylation: Assembly
36
Intermediate filament Types
- Nuclear IF (lamin A/B/C) - Epithelial IF (keratin) - Vimentin-like IF (vimentin, desmin in muscle) - Axonal IF (neurofilaments & axon diameter)
37
3 Families of Motor Proteins
- Myosin (actin associated) - Kinesin (MT associated) - Dyenin (MT associated)
38
Motor Proteins Domain Structures
- Motor domain: head, binds cytoskeleton (ATPase act.) - Neck: associated light chains (regulator light chain binding) - Tail domain: binds cargo
39
Myosin Types
(18 types in eukaryotes) - Myosin I - Myosin II - Myosin V
40
Myosin I
- Found in cell cortex - One-headed - Tail binds plasma membrane - Calmodulin-dep. light chains - IC organization & protrusion of actin-rich structures like microvilli at cell surface
41
Myosin V
Vesicle & organelle transport - Dimer structure with 2 head domains that can move along filaments - Calmodulin-dep. light chains
42
Myosin II
Contractile activity (cytokinesis & cell migration) - Assemble into thick filaments with hundreds of heads (2 each) - ATP binding releases head from filament - ATP hydrolysis causes head to bind to actin with ADP+Pi & power stroke
43
Myosin Regulation
- Tropomyosin: covers myosin binding sites on Actin - Troponin (T, I, C) - MLCK
44
Kinesin
Walks towards + end of Microtubule with leading & trailing head - 2 heavy & 2 light chains - Transport vesicles - Sister chromatids separation
45
Dynein (& types)
Walks toward - end of Microtubule towards Centrosome - 1/2/3 heavy chains & variable light chains - Cytoplasmic Dyneins: transport of organelles - Axonemal Dyneins: sliding movement of Cilia & flagella (beating)
46
Cytoplasmic Dyneins
- Type 1: Organelle trafficking towards centrosome - Type 2: Transports material from tip of cilia to base
47
Largest & one of fastest molecular motors
Dyneins
48
Griscelli Syndrome
Problem with Myosin V causing issue with melanin vesicle transport to keratinocytes = Hypopigmentation
49
Vesicular Transport Mechanism
1) Budding 2) Translocation 3) Fusion
50
Protein covering Transport Vesicle
Non-specific for substances & not bound to membrane - Clathrin: endocytosis & lysosomal T - COP I: cis-golgi to RER (retrograde) - COP II: RER to cis-golgi (anterograde)
51
Adaptor proteins vesicle
Substance specific & binds both membrane & coat proteins - Monomer (clathrin) - Heterotetramer (CopI/II)
52
Rab Protiens
Non-specific for substances & bound to membrane (prenylation of 2 Cys) - Small GTPase - Vesicle formation & fusion - Provide Energy for vesicle migration - 5 conserved motifs for GTP-binding
53
Rab-GDP/GTP
- Rab-GDP: Inactive & cytosolic - Rab-GTP: Active & membrane bound
54
Rab Proteins G motifs
- G1: Nucleotide binding - G2: GTP/GDP - G3: Mg2+ binding - G4: H-bond - G5: Nucleotide binding
55
Rab Cycle
1) Rab-GDP is inactive 2) Rab-GDP meets REP (rab escort) transferring a Prenyl group (lipid) to Rab & brings Rab to donor membrane (for GEF) 3) GEF activates to GTP, Rab binds vesicle & motor protein 4) Rab helps fusion of vesicle with target via SNAREs 5) GAP inactivates Rab 6) GDI transports Rab-GDP back to membrane 7) If Rab returns with GDI not REP then GDF removes GDI
56
Clathrin structure
- Triskelion - 3 Heavy chains - 3 Central light chains - Distal & proximal legs - Globular domain made of Linker region (a-helical) & N-terminal (7 bladed B-propeller) which recognizes adaptor proteins
57
Clathrin adaptor protein (& types)
Adaptin (AP) - AP1: trans-golgi, carries lysosomal hydrolase - AP2: PM, endocytosis - AP3: Transport to lysosomes - AP4 (less known)
58
What forms Vesicle inner coat layer (clathrin)
- Cargo receptor - Adaptin complex
59
Vesicle structures/shapes
- Mini coat (4 hex.) - Hexagonal barrel (8 hex.) - Soccer ball (20 hex.) (all 12 pentagons + Hex)
60
Clathrin functions, only vesicle?
- Non dividing cells for Clathrin-mediated endocytosis - Dividing cell: Forms part of spindle apparatus, no clathrin coated vesicles
61
Dynamin
Cytosolic protein which catalyzes budding of vesicle from PM - PI binding domain - GTPase activity squeezes neck of vesicle
62
Clathrin Vesicle formation
1) Nucleation: adaptor binds membrane & helper p., cargo, clathrin binds adaptor & helper 2) Invagination: polymerization & more clathrins recruited 3) Complete assembly: attachment of BAR domain containing protein at neck on invag. 4) Vesicle Scission: SH3 domain of BAR recruits Dynamin which squeezes neck by hydrolyzing GTP 5) Vesicle uncoating before transport
63
Uncoating of Clathrin Vesicle
Hsc70-ATP auxillin - Hydrolyzes ATP and uses energy to peel off clathrin coat from vesicle
64
COP I structure
- Heteroheptamer (a,B,...) - ARF not part of heptamer (ADP ribosylation factor, Ras) - ARF active when GTP bound (attaches to membrane by myristoilation) and assembles COP1 coat on cis-Golgi
65
COP I vesicle formation
1) ARF-GDP inactive (p23 bound) 2) GEF Sec7 activates ARF to GTP & p23 released binding p24 for coatomer 3) ARF bind membrane and recruits COP1 complex (trimerization) 4) Cargo recognized by a/B' subunits & ARF/COP1 5) Budding off Golgi by BAR-domain proteins & DAG 6) No uncoating till vesicle reaches ER??? (maybe not) 7) GAP inactivates ARF = fusion
66
COP II structure
- Heteroheptamer (Sar/Sec,...) - Sar1: Ras protein part of COP2 - Sar1-GTP is active (attached to membrane by amphipathic helix)
67
COP II vesicle formation
1) Sar1-GDP inactive 2) GEF Sec12 activates Sar1 (GTP) 3) Sar1 binds ER & recruits prebudding complex adaptor complex (sec24/23) for Inner coat 4) Sec23 binds Sar1, Sec24 to cargo 5) Coat proteins (sec13,31) bind the prebudding complex for Outer coat 6) Polymerization of COP2 7) Budding off of ER membrane by ERES 8) No uncoating till golgi??? 9) Sec23 (GAP) inactivates Sar1 (GDP)
68
Tethering of vesicle to membrane steps
1) Recognition by Rab binding tethering p 2) Docking: tethering protein pulls vesicle closer so SNAREs interact (v/t snares) attracting SNAPS & NSF 3) Fusion: SNAREs force lipid bilayer to merge (ATP)
69
SNAPs & NSF
- SNAP: Stabilizes the SNARE complex - NSF: ATPase for energy to disassemble SNAREs
70
SNARE disassembly
- Requires ATP because cis-SNARE (combined T/V) is more energetically favorable - Use SNAPs & NsF to disassemble - Thioesterase cleaves t-SNARE to free because T has cys-palmitoylation which is reversible
71
SNARE protein types
- v/t SNARES - Q-SNARE: Gln in 0 position of zero ionic layer (3) - R-SNARE: Arg in 0 position of zero ionic layer (1)
72
SNARE protein info
>60 SNARE types - Organelle specific
73
Trans-SNARE complex
- V/T-SNARE on membranes - Extra t-SNARE in between & form connection by palmitoylation (reversible)
74
Types of vesicle fusion models
- Kiss and run - Extended kiss & run - Full fusion of vesicle
75
Types of Cellular transport GENERAL
- Along con. gradient: Physico-chemical energy (passive or facilitated diffusion) - Against conc. gradient: Chemical energy (1'/2' T, vesicular T)
76
Transport based on Direction
- Exocytosis (regulated & constitutive) - Endocytosis (transcytosis & potocytosis)
77
Transport based on State
- Phagocytosis - Pinocytosis (macro/micro)
78
Main vesicular pathways
- Anterograde (ER to Golgi by COP2) - Retrograde (Golgi to ER by COP1) - Lysosomal T (trans-Golgi to early endosome) - Endocytosis (EC to early endosome) - Residual Body - Exocytosis - Transcytosis (glucose)
79
Proteins involved in Clathrin-mediated Endocytosis
- Dynamins (pinching) - HIP1R (aids membrane folding) - Cortactin (induces ARP2/3) - ARP2/3 (on actin to internalize vesicle)
80
Types of Exocytosis
- Constitutive (non-regulated, stuff like PM proteins) - Regulated (hormones)
81
Proteome
Entire set of proteins expressed by a genome, cell, tissue or organism at a certain time
82
Proteome classifications
- Tissue-specific Proteome - House-keeping Proteome - Regulatory Proteome (gene exp.) - Secretome (GFs, Cytokines)
83
Nucleus Proteome
- TFs, DNA/RNA polymerases, Histones, Nuclear pore complex proteins - Proteins for chromatin organization, HAT/DAC, DNA repair proteins, Nuclear export/import
84
ER Proteome
Responsible for protein synthesis, folding, modification, & lipid biosynthesis (3% of total) - Chaperones - ER-resident enzymes (glucosidases) - ERAD components
85
Golgi Proteome
Protein modification, sorting, trafficking (vesicles) - Glycosylation enzymes - Golgi matrix proteins - COP1 / COP2
86
Mitochondria Proteome
ETC, ATP synthesis, ... - ETC complexes - TCA enzymes - Mitochondrial import machinery (TOM/TIM) - Matrix has 2/3 of m.proteins
87
Lysosome Proteome
- Digestive enzymes (peptidases, phosphatases, glucosidases) - Low pH - Proton pump (ATPase)
88
Peroxisome Proteome
- Oxygenase enzymes using oxygen to reduce organic substrate - Can produce H2O2, eliminated by enzyme catalse
89
Protein sorting
Fate of a protein depends on their a.a sequence which contain sorting/localization signals recognized by receptors and transported to destination
90
3 different movements of Proteins
- Gated transport (cytosol-nucleus) - Protein Translocation - Vesicular transport
91
Conditions for Protein Sorting
- Signal sequences - Translocation machinery - Chaperones & Cofactors - Post-translational modifications - Organelle specific sorting signals (NLS) - Vesicular Transport - Golgi apparatus - ER quality control
92
Types of Signals on Proteins
- Signal Sequence (AA) - Signal Patch (NLS)
93
Types of Signals proteins to (nuc/mit/ER)
- Import to Nucleus (positive AA) - Import to Mitochondria (amphipathic) - Import to ER (hydrophobic A.A on N-term)
94
ER protein Synthesis
Co-translational Translocation - Basically as the protein is synthesized by the ribosome in cytosol, as soon as signal (hydrophobic) is translated, the SRP stops the ribosome and translocates it to ER membrane through translocon channel (Sec61)
95
Protein translation direction
N to C terminal
96
How transmembrane proteins are synthesized
They have a Stop transfer sequence (hydrophobic) - As protein is synthesized through channel (Sec61) the STS is reached which tells channel leave me in - N terminal in ER (synthed. first), C terminal stays in cytosol
97
Proteins that pierce membrane more than once
Have start & stop signals after each other based on how many times in and out (e.g. GPCR 7TM)
98
Protein targeting to mitochondria
Requires an Amphipathic a-helix signal - Hydrophobic AAs on one side - Hydrophilic AAs on the other
99
Outer Mitochondrial Membrane Transporters
- TOM: Transport from cytosol to intermembrane space - SAM: Helps fold outer membrane and place TM proteins in membrane
100
Inner Mitochondrial Membrane Transporters
- TIM23: Transports proteins into the matrix & helps TM insertion - TIM22: AIds in insertion of TM proteins - OXA: Also aids in TM insertion
101
Mitochondrial targeting mechanism
1) Amphipathic a-helix recognized by TOM complex 2) Protein enters TOM after Hsp70 chaperone removal (ATP) 3) Enters TIM23 4) Once inside mitochondria, mitochondrial Hsp70 binds, signal is cleaved 5) Protein forms tertiary structure using mitochondrial chaperones (Requires energy)
102
Peroxisomal Targeting Signals
- C-terminal tripeptides (PTS1 on Pex5) - N-terminal Nonapeptides (PTS2 on Pex7/18)
103
Protein targeting into Peroxisome
- Signals PTS1/2 - Recognized by cytosolic proteins = Pex5, Pex7/18 like importin - As they bind target they move to form a pore, moves in in folded state so dont have to unfolded
104
Peroxisome targeting mechanism
1) PTS1 (c-term, Ser-Lys-Leu) recognized by Pex5 and carries cargo to peroxisome 2) Then ubiquitinated to release cargo to peroxisome matrix 3) Pex5 returns to cytosol where ubiq is removed (pex7/18 recognize N-term PTS2)
105
What do Pex do in Peroxisome
Once PTS binds, they form pores to allow ONLY fully folded proteins to enter
106
Uptake of substrate into Lysosome
- Mainly from trans-Golgi network - Signal has sugar with Pi group attached - Packaged into vesicles and sent to lysosome from ER via Golgi
107
Pathways of Uptake of substrate into Lysosome
- Endocytosis to early/late Endosome that can fuse with lysosome - Phagocytosis to Phagosome to phagolysosome - Autophagy to autophagosome to lysosome (all mediated by SNAREs)
108
What is the only Organelle that gets its Proteome through Gated transport?
Nucleus
109
Nuclear Pore structure
- 110mDa - ~1000 proteins make up nuclear pore complex - ~30 different Nucleoporins make it (Nups) - Regulated by Ran proteins - <60kDa can pass
110
Layers of NPC
- Membrane layer - Scaffold Layer - FG Nups layer (30 nucleoporins) - 2 Rings: Cytoplasmic & Nuclear (basket)
111
How does the nucleus know which proteins should enter/exit the NPC?
Nuclear import receptors Importins/Exportins which recognize NLS characterized by positive a.a Arginine/Lysine
112
Mechanism of Intracellular Gated nuclear IMPORT
1) NLS (cargo) recognized by importin 2) Importin recognized by cytosolic fibers 3) Ran-GTP binds once inside to release cargo protein 4) Ran-GTP takes importin back to cytosol and turns to GDP to leave it 5) Importin ready for new Cargo
113
Mechanism of Intracellular Gated nuclear EXPORT
1) NES Exportin binds Ran-GTP 2) Then Exportin binds Cargo 3) Passage through pore 4) GTP to GDP in cytosol to release Cargo 5) Exportin back to Nucleus
114
What converts Ran-GTP to Ran-GDP and vice versa?
Ran-GAP and Ran-GEF
115
Transport through FG-Nup
- FG: Phenylalanine-Glycine both Hydrophobic - Importin also Hydrophobic - Passes through with hydrophobic-hydrophobic interactions
116
Calcineurin in high Ca2+
1) Ca2+ activates Calcineurin 2) Calcineurin is a protein phosphatase 3) Exposes NLS and block NES
117
Which organelles use Transmembrane Transport?
- ER - Mitochondria
118
What proteins are synthesized in Mitochondria
ETC proteins (all rest come from cytosol)
119
TOM (mitochondria)
- Allow transfer of cytosol translated proteins - Uses amphipathic α-helix signal - Recognized by recognition molecules on mitochondrial memb. (OMM)
120
SAM (mitochondria)
Helps folding of outer membrane proteins for TM insertion (OMM)
121
TIM23 (mitochondria)
- Transports proteins into the matrix and helps insertion of transmembrane proteins - Spans 2 membranes due to elongated hydrophobic part (IMM)
122
Are proteins to be transported into Mitochondria folded?
They are Unfolded because the channels are Tiny, so chaperones keep them unfolded till they reach TOM
123
Steps of Mitochondrial Import
1) Amphipathic a-helix signal recognized by receptor on TOM 2) Protein now in IM space 3) TIM23 allows into IMM 4) Signal cleaved by peptidase Only import, they cant export due to size
124
How does mitochondria import get its energy?
- The chaperones that hold protein in unfolded state are Hsp70 which are found in an ATP-bound state - When they pass to IM space there are mtHsp70 that do the same - They dissociate the protein in matrix
125
Co-Translational Translocation (ER)
1) Translation starts in Cytosol 2) Stops at a point N-term. sig binds SRP 3) Ribosome associates with ER using SRP and continues translation 4) The polypeptide is pushed into the ER as it is synthesized through Translocator channel (from Sec61) No way to come out after folding
126
SRP parts
- Signal sequence binding pocket - Translational pause domain - Hinge domain
127
ER stress caused by
- Biotransformation processes (p450 making ROS) - Disulfide bond formation (H2O2 forms) - Misfolded proteins (accumulation in ER)
128
UPR 2 Phases (unfolded protein response)
1) Tries to increase protein folding capacity to remove ER stress and decrease misfolded proteins 2) If stress can not be removed, UPR promotes ER stress-induced Apoptosis
129
PERK (PKR like ER kinase)
1) Accumulation of misfolded proteins triggers PERK 2) Phosph. and inactivates eIF2 3) ATF4 synth still occuring 4) ATF4 induces other TF CHOP (pro-apoptotic TF) 5) CHOP has many results
130
CHOP results (PERK)
- Inhibition of Bcl-2, Bak & Bax released and active - Induce pro-apop. BH3-only proteins (like BIM) for pore formation & CytC - GADD34 activation, dephosph. eIF2 so translation not inhibited - Increased D5R expression (death-R) which activates procaspases
131
IRE-1
1) Mostly Pro-survival: Creates spliced mRNA translated to transcription regulatory protein XBP1, activates genes in nucleus to mediate UPR 2) Pro-death: MAPK cascade, activate Bak/Bax, intrinsic apoptosis path
132
ATF-6
When misfolded proteins accumulate ATF6 is translocated to Golgi where it undergoes proteolysis, cytosolic domain removed, can go to nucleus and induce UPR proteins synth.
133
What regulates mediators of UPR
BiP (binding immunoglobulin protein) binds them when they are not needed & dissociates when proteins accumulate then binding the misfolded proteins
134
N-Glycosylation Protein Control
1) Proteins in ER labelled with glucose side chain (3) 2) Glucosidases take off 2 and keep 1 glucose on protein 3) Glucose allows Calnexin/Calreticulin to bind (chaperones) 4) After folding, glucosidase removes last glucose 5) If still misfolded Glucosyl transferase adds UDP-Glucose to allow further folding
135
ERAD (ER associated degradation)
- Used to eliminate misfolded secretory proteins from the ER since no Proteosome - Misfolded protein taken from ER back to cytosol in retro-translocation - Ubiq-Proteasome system deg.
136
In ERAD why do we have Retro-translocation
The ER does not have proteasomes so the misfolded protein must be taken to cytosol
137
Metabolome
Total number of metabolites present within an organ/tissue/cell
138
pH values in Cell (Cell / Nuc / Mit / Lys)
- Cell = 7.2 - Nucleus = 7.2 - Mitochondria = 8 (ATP pumped out) - Lysosome = 4.7 (H+ inside)
139
Ca2+ balance in Cell
- Membrane: PMCA & NCX - ER: SERCA
140
Cell redox condition systems
- Glutathione system - Thioredoxin system
141
Glutathione system
Glutathione is a Tripeptide composed of Glutamine, Cysteine, Glycine acting as major Antioxidant in cells - Glutathione Reductase regenerates GSH from oxidized form GSSG utilizing NADPH for this
142
Thioredoxin system
Thioredoxins act as antioxidants by reducing disulfide bonds in proteins so reversing oxidative modifications like Cys-S-S-Cys - Thioredoxin Reductase regenerates Thioredoxin using NADPH
143
Can NADPH freely cross membrane?
No Only shuttling of electrons used to regenerate them inside ER / Mitochondria (malate-aspartate shuttle & glycerol 3P D.H mitoch/cytoplasm)
144
Mitochondria role in Antioxidants
Produces 3 NADH in CAC
145
Cell FA balance
- FA transported to mitochondria using FA-carnitine - Rate limiting step is Acetyl-coa to Malonyl-coa - Malonyl-coa inhibits transfer of FA into mitochondria - FA synth in cytosol - FA ox in Mitochondria
146
HMG-CoA in Mitochondria/Cytosol
- Mitochondria: Involved in Ketone body production (HMG-Coa Lyase) - Cytosol: Cholesterol synth. (HMG-coa reductase)
147
Heme biosynthesis places
Starts in mitochondria, then to Cytosol, and ends in Mitochondria again (Heme used as prosthetic in ETC proteins)
148
Urea Cycle
Ammonium generated by: - Glutamate DH - Glutaminase To Carbamoyl phosphate then Citrulline taken out of Mitochondria
149
AMPK consequences
- Phosph. ULK-1 & JNK which effect Beclin-1 = Autophagy (macro) - Activates TSC1/2 (GAP) blocking mTORC activating ULK-1
150
ROS elimination
- Peroxisome: Superoxide dismutase makes H2O2 from 2 superoxides, then catalase to water & O2 - Mitochondria: Glutathione & Thioredoxin system form water with NADPH
151
Mitochondrial Dysfuntion Types
- Primary: Genetic mutation of proteins - Secondary: Due to ROS (can cause CytC release = apoptosis)
152
Peroxisome Anabolic & Catabolic
- Catabolic: B-oxidation of VLCFA & a-oxidation of BCFA - Anabolic: Bile acid synth, De novo Lipogenesis, Cholesterol Synth (not 100%)
153
ECM Composed of 3 Major macormolecules
- Structural fibrous proteins: Elastin & Fibrilin - Glycoproteins: Fibronectin & Laminin - Glycosaminoglycans: Hyaluronan, Heparan Sulfate, Chondroitin Sulfate
154
Elastin
- No hydroxyproline like Collagen, fewer H-bonds, not as strong/rigid - Glycine / Valine / Proline - Glycine every 3rd a.a (like collagen) - Blood vessels, lungs
155
Hyaluronic Acid (building blocks)
- Made up of Glucaronic acid & N-acetyl-Glucosamine building blocks - High water binding capacity (OH)
156
Cell surface receptors
- Integrin receptors - Ephrin receptors - Notch / Delta receptors
157
Cell adhesion molecules
- Cadherins (Ca2+ dep.) - Selectins (Ca2+ dep.) - Ig family (CAMs)
158
Cell-Cell interaction
1) Ligand binds integrin-R 2) B-subunit of R binds Focal Adhesion Kinase 3) Autophosphorylation leads to: - Grb/SOS cascade - PI3K for survival - Paxilin, Cdc42, Rac, Rho for Actin cell movement
159
Integrin Receptor
- In All cells - Heterodimer (a, B) - N-term. is E.C, C-term is I.C - E.C domain binds RGD sequence on Fibronectin, Collagen, Laminin
160
Ephrin Receptors & Notch / Delta Receptors
- Cell-cell bidirectional signaling - Development - Cancer signaling - Neurogen, Angiogen, bone remod.
161
Metastasis Phases
1) Release: proteases cut connections bw cells to free cancers, E-cadherin reduced, MMP activation, avB3 integrin for invadopodia formation 2) Migration: Cancer in blood & lymph, induces angiogenesis 3) Homing: Exit blood & proliferates in tissue
162
Invadopodium
Marker of Metastasis - Secretes proteases that break cell-cell connection - avB3 integrin-R
163
Epithelial-Mesenchymal transition
Important step in Metastasis as mesenchymal cells are more migratory & resistant to Chemotherapy - Downregulated E-cadherin, less adhesion - Invapodium form to degrade ECM - Migrate, and during homing can form epithelial cells again to proliferate
164
2 Main states of Cancer stem cells
- Slowly Asymmetrical dividing state - Rapidly Symmetrical dividing state
165
Cell culturing
Growing cells under controlled conditions outside their natural environment
166
Types of Cell culturing
- Primary culture: directly from tissue - Cell culture: divisions of a primary culture after 40-50 passes - Cell line: Culture developed from 1 single cell so all identical genetically
167
HeLa Cells
Immortal cell line from Cervical cancer that can keep dividing infinitely
168
How to maintain Cell cultures
- Optimum growth Temp - Constant pCO2 - Adequate Humidity - Sterile conditions
169
How to freeze cell culture
Temperature drop of 1˚ per minute but defrosting as quick as possible
170
Cell fractionation
Separation of cellular compartments for study individually separated by Centrifugation after Homogenization
171
Possible ways to homogenize in cell fractionation
- Osmotic shock (swell & burst) - Knife hom. (detergent/bile) - Ultrasound - "French press" (can be mild or rough)
172
In vivo microscopy
Performed on living cells using non-toxic marker that is compatible with physiology of cell (fusion proteins)
173
Light microscope Limitations
- Only dark or highly reflective surfaces can be seen - Very limited resolution due to diffraction - Points out of the focus frame reduces clarity of image
174
What can we use to view details for In Vivo microscopy?
Fluorescence microscopy
175
Flow Cytometry
For fast multi-parameter testing by using mixed cell populations and each cell type can be separately measured, analyzed, and separated by phenotype or functional state
176
Flow cytometry method
Sheath fluid surrounds sample fluid in a narrow single-file stream & it passes through highly focused light source & optical signals can be measured
177
Flow cytometry used for
- Monitor Apoptosis & changes of DNA content - DNA distribution to see cells in different phases of cell cycle
178
FACS
Fluorescence Activated Cell Sorting - Specialized type of flow cytometry - Method for sorting heterogenous mixture of cells into containers one cell at a time based on light scattering - Done by an electrostatic deflection system that diverts droplets into containers based on their charge

MCB (6 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions