6. Transporting Process Flashcards

(107 cards)

1
Q

What are the definitions of Passive transport and Active Transport

A

Passive Transport: No energy required; moves down a gradient.
Active Transport: Requires energy (ATP); moves against a gradient.

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2
Q

Definition

Active Transport

A

Active transport is the movement of molecules across a membrane using cellular energy (usually ATP) to move substances against their concentration or electrochemical gradient.

JP補足:ATPを使って濃度勾配に逆らう輸送。

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3
Q

Passive Transport

A

Passive transport is the movement of molecules across a membrane without the use of cellular energy, occurring down their concentration or electrochemical gradient.

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4
Q

Osmosis

A

Osmosis is the** passive movement of water **across a selectively permeable membrane from a region of lower solute concentration to higher solute concentration.

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5
Q

Transporter

A

A transporter is a membrane protein that undergoes conformational changes to move specific molecules across a membrane, either passively or actively.

JP補足:形を変えて物質を運ぶタンパク質。

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6
Q

Difinition

Uniporter

A

A uniporter is a transporter that moves one specific type of molecule across a membrane in one direction.

JP補足:単一の物質だけを一方向に運ぶ。

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7
Q

Difinition

Cotransporter

A

Including Symporter and Antiporter
A cotransporter moves two or more different molecules simultaneously across a membrane, with transport coupled.

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8
Q

Difinition

Symporter

A

A cotransporter moving two molecules in the same direction.

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9
Q

Difinition

What is an antiporter?

A

A cotransporter moving molecules in opposite directions.

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10
Q

Difinition

Facilitated Diffusion

A

passive transport in which molecules move across a membrane through** specific transport proteins**, down their gradient.

タンパク質を使うが、ATPを使わない拡散

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11
Q

Aquaporin

A

A water-specific channel protein that increases water transport.

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12
Q

What is Ion Pump

A

a membrane protein that uses energy (often ATP) to move ions across a membrane against their electrochemical gradients.

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13
Q

Chemical Gradient

A

Difference in solute concentration across a membrane.

濃度の差。

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14
Q

What is an electrical gradient?

A

Difference in** charge/electric potential **across a membrane.

Normal Electrical gradient (-70mV)

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15
Q

What is an electrochemical gradient?

A

Combined effect of the chemical and electrical gradients that drives ion movement.

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16
Q

What is a channel protein?

A

a type of integral membrane protein that forms a pore or channel through the cell membrane, allowing specific ions, molecules, or signals to pass through via facilitated diffusion

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17
Q

What is ATP-driven active transport (ATP gated)?
List the examples

A

Type of **Primary acrive transport **using ATP hydrolysis directly to to pump molecules or ions against a gradient.

Ex) Na+ / K+ Pump, Ca+ pump, ABC transporters

ATP分解のエネルギーを直接利用。

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18
Q

What is ion gradient–driven active transport?
also list an example.

A

Secondary active transport powered by the energy stored in an ion gradient (generated by ATP pump) to drive the transport of another molecule against its gradient.

Ex. Na+ / Ca+ pump

ATPを直接使わない!イオンの“流れ落ちる力”を利用して物質を運ぶ。

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19
Q

What does the Na⁺/K⁺ pump do?

A

ATP-dependent antiporter that pumps** 3 Na⁺ ions out of the cell and 2 K⁺ ions in**, maintaining membrane potential (-70 mV) and ion gradients.

3Na⁺を外へ、2K⁺を内へ。ATP使用。

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20
Q

What does the** Ca²⁺ pump** do?

A

The Ca²⁺ pump (Ca²⁺-ATPase) uses ATP to transport Ca²⁺ ions out of the cytosol, usually into the extracellular space or ER, maintaining low cytosolic Ca²⁺ levels.

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21
Q

What does the Na⁺/Ca²⁺ exchanger do?

A

The Na⁺/Ca²⁺ exchanger uses the inward Na⁺ gradient to drive the export of Ca²⁺ from the cell, functioning as a secondary active antiporter.

Na⁺が入る力でCa²⁺を外に出す。ATPは直接使わない。

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22
Q

Protein targeting (sorting)

A

Directing newly synthesized proteins to specific cellular destinations using signal sequences.

新しく作られたタンパク質が どの細胞内区画へ送られるかを決める仕組み。住所ラベル=シグナル配列で送り先を指定。

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23
Q

Secretory route

A

Pathway where proteins enter the ER, then move through the Golgi to the membrane lysosomes or secretion.

ER→Golgi→細胞外 or 膜 or リソソーム へ向かうタンパク質の運搬ルート。

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24
Q

Non-secretory route (pathway)
Also draw the rough picture.

A

Pathway where proteins remain in the cytosol or go to membrane of organelles, such as mitochondria, nucleus, and peroxisomes (also membrane of ER) without entering the ER.

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25
**Signal sequence** Also draw the rough picture
A short peptide that directs a protein to a specific cellular compartment. ## Footnote (→ often 20-50 AA) タンパク質に付いた 配送ラベル(住所)
26
**Signal Recognition Particle (SRP)**
A cytosolic **ribonucleoprotein **complex that binds ER signal sequences and pauses translation for ER targeting (until the ribosome docks at the ER membrane.) ## Footnote ER向けのシグナルを認識して 翻訳を一時停止し、ERへ誘導 する因子。
27
**SRP receptor**
An ER membrane receptor that binds SRP–ribosome complexes to initiate translocation into ER. ## Footnote ER膜にある SRPのreceptor。ここで翻訳が再開し、ER内へ送り込む。
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**Translocation**
Movement of a newely synthesized polypeptide across a membrane into an organelle such as ER. ## Footnote タンパク質を膜の向こう側へ通すこと。
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**Signal peptidase
A transmembrane ER enzyme (associated with translocon) that remove (cut) signal sequences after translocation. ## Footnote ERに入った後に シグナル配列を切り取る酵素。
30
**ER signal sequence**
An N-terminal sequence directing proteins to the ER for co-translational import. ## Footnote ER配送専用のシグナル。N末にあることが多い。
31
**Ribonucleoprotein (RNP)**
A complex composed of RNA and protein,such as the SRP. ## Footnote RNA+タンパク質複合体。SRPもこれ。
32
Topological classes of membrane proteins
Categories describing how membrane proteins span and orient within the lipid bilayer. number of times that its polypeptide chain spans the membrane and the orientation of these membrane-spanning segments within the membrane - How many times a protein spans the membrane - Orientation of its transmembrane (TM) segments Membrane-spanning regions: * Typically 20–25 hydrophobic amino acids forming an α-helix * Hydrophobic side chains face lipid bilayer interior ## Footnote 膜タンパク質が “どちら向き” に、どんな形で膜を貫いているか = 構造上の配置 タンパク質が膜を何回貫通するのか? どの部分が細胞外?どの部分が細胞内? どんな anchoring(固定)で膜にくっついているのか?
33
Signal-anchor sequence
An internal sequence acting both as an ER signal and a membrane anchor. ## Footnote Type II & IIIに見つかる
34
Stop-transfer sequence
A sequence that halts translocation and anchors the protein in the membrane. ## Footnote Type Iで見つかる
35
ER lumen
The internal space of the ER where protein folding and modification occur.
36
Amphipathic
Having both hydrophobic and hydrophilic regions.
37
Cytosol
The aqueous interior of the cell excluding organelles.
38
Transport vesicle
A membrane-bound vesicle that moves cargo between organelles.
39
Vesicular transport
Transport using membrane vesicles to move proteins and lipids between compartments.
40
Golgi cisterns
Flattened membrane sacs that modify and process transported proteins. 1️⃣ cis-Golgi(シス) ER から来た vesicle を受け取る入口側 タンパクの初期修飾(マンノース除去など) 2️⃣ medial-Golgi(中間) 糖鎖の追加修飾 複雑な glycosylation 3️⃣ trans-Golgi(トランス) 最終的な糖鎖修飾 タンパク質の仕分けが始まる 4️⃣ TGN(trans-Golgi network) 最終仕分けセンター リソソーム行き 分泌経路 細胞膜行き **cis(入り口) → medial(加工) → trans(仕上げ) → TGN(配送)** - なぜ “cisterns” が大事なの? Because: ✔ 各 cistern は 違う酵素セット を持っていて、  タンパク質は順に移動しながら加工されていく → **ゴルジ体は「流れベルトコンベア工場」**になっている。
41
Golgi network
Entry (cis) and exit (trans) regions of the Golgi responsible for protein sorting.
42
Endocytosis
Cellular uptake of extracellular material through vesicle formation.
43
List the example of Non-selective Endocytosys
1. **Phagocytosis** - Occurs in specialized cells (e.g., macrophages) - Engulfs large particles or bacteria - Forms **phagosomes** - Actin-dependent and **nonselective** **2. Pinocytosis** - Found in all eukaryotic cells - Nonselective uptake of extracellular fluid and dissolved material
44
Explain the receptor mediated Endocytosis
- Highly specific - A receptor binds a specific ligand → internalization **Examples of internalized ligands:** - **Low-density lipoprotein (LDL)** - **Transferrin** (iron carrier) - **Protein hormones** (e.g., insulin) - **Certain glycoproteins** Mechanism: 1. Ligand binds receptor at plasma membrane 2. Receptor-ligand complex clusters 3. Plasma membrane invaginates 4. Vesicle pinches off and enters the endocytic pathway
45
Importin
A transport receptor that binds NLS-containing proteins and imports them into the nucleus.
46
Exportin
A receptor that exports NES-containing proteins from the nucleus.
47
Ran
A small GTP-binding protein controlling nuclear import and export.
48
Ran-GTP
The active form of Ran that regulates cargo release and receptor binding.
49
Ran-GEF
A nuclear factor converting Ran–GDP to Ran–GTP. ## Footnote GEF: Guanin Exchange Factor
50
Ran-GAP
A cytosolic protein that hydrolyzes Ran–GTP to Ran–GDP.
51
Cargo
A protein with a localization signal transported by importins or exportins. Cargo proteins は、vesicle によって特定の細胞内コンパートメントへ運ばれる「荷物タンパク質」。 配送先はタンパク質がもつ signal sequence(sorting signal)によって決まる。
52
NLS
Nuclear localization sequence directing proteins into the nucleus by binding with Importin A and B
53
NES
Nuclear export signal directing proteins out of the nucleus with Cargocomplex (Ran GTP+Cargoprotein+NES+Exportin 1)
54
Exporter mRNA complex
A complex mediating nuclear export of processed mRNA. (mRNA-hnRNP Complex + CBC(Cap Binding Complex at 5' end))
55
Write the Pathway of Protein Import and Export to the nucleus
56
Write the pathway of mRNA export from nucleus
**III. Export of mRNAs from the Nucleus** **1. 5’ End Leads Transport** - The fully processed **mRNP (mRNA–hnRNP complex)** associates with the **cap-binding complex (CBC)** at the 5′ end. - CBC passes through NPC **first**. --- **2. Removal of Nuclear-Restricted hnRNPs** - Certain hnRNP proteins (orange & dark blue in the diagram) remain **nucleus-restricted**. - These are removed during NPC transport because they **lack NES** → they would otherwise retain mRNA inside the nucleus. --- **3. NES-Containing hnRNPs Mediate Export** - hnRNPs containing **NES** bind export machinery (exportin 1 + Ran·GTP). - They escort the mRNA through the NPC into the cytoplasm. --- **4. Cytoplasmic Events** - Cytoplasmic **RanGAP** triggers GTP hydrolysis by Ran. - Shuttling hnRNPs dissociate from export receptors. - They return to the nucleus for the next cycle. --- **5. mRNA Matures for Cytoplasmic Function** - Freed mRNA associates with cytosolic mRNP proteins. - Example: **Poly(A)-binding protein (PABP)** binds the 3′ poly(A) tail → preparing mRNA for translation.
57
What are the functions of **SPR & SPR Receptor**
1. Help maintain interaction of nascent secretory protein and ER membrane 2. Act together to permit elongation and synthesis of complete protein (only when ER membrane present) 3. Bring ribosomes that are synthesizing secretory proteins to ER membrane
58
Where do the SPR transiently binds to?
1. ER signal sequence 2. Ribosome 3. SPR receptor ## Footnote 6 discrete (indivisual) polypeptide 300 nucleotide RNAでできてる ->
59
What are the three types of protein modification during **secreting pathway**?
1. **Glycosylation:** Addition and processing of carbohydrates (ER & Golgi) 2. **Disulfide bond formation:** Occurs in the ER 3. **Protein folding and assembly:** Occurs in the ER 4. **Proteolytic cleavage:** Occurs in ER, Golgi, and secretory vesicles
60
List the two types of glycoprotein and their characteristics
- **O-linked oligosaccharides** - Attached to **Serine/Threonine hydroxyl groups** - Often short (1–4 sugars) - Seen in **collagen, glycophorin** - **N-linked oligosaccharides** - Attached to **Asn (Asparagine) amide nitrogen -NH基** - CHARACTERISTICS:Larger, branched, complex - WHERE:Initial synthesis occurs in the **ER**
61
What is the structure of precursur of N-linked precursur
- Universal precursor in plants, animals, and yeast: - **3 glucose (Glc)** - **9 mannose (Man)** - **2 N-acetylglucosamine (GlcNAc)** - Total = **14-residue oligosaccharide** - Added as a **preformed block** in the rough ER
62
What is the function of N-linked oligosaccharides
1. Required for **proper folding** in the ER (⇒ Quality Control) 2. Contribute to **stability** of many secreted glycoproteins 3. Essential for **cell–cell adhesion** (e.g., cell-surface glycoproteins) 4. Can **induce immune responses** (e.g., oligosaccharide antigens)
63
During protein modification of secretory pathway, disulfide bond formation is done by
**Protein Disulfide Isomerase (PDI)** ## Footnote abundunt in ER of secretory organs (liver, pancreas) Present in all eukaryotic cells
64
Disulfide bond is formed between
**Cysteins** -SH 基を持っている
65
List the proteins involved in protein folding
1. Chaperon : BiP (Binding Immunoglobulin Protein) 2. Lectines : calnexin, calreticulin 3. PDI (protein disulfide isomerase) : disulfide bridge formation 4. Oligosaccharyl transferase: glycosylation 5. Peptidyleprolyl isomerase: prolin cis-trans transformation
66
secretory pathwayの流れを書く
## Footnote ノート参照
67
Cisterna progression
cisterna physically moves through the Golgi. cis-, medial-, trans- Golgi to trans-Golgi network ## Footnote No involving **Anterograde vesicle** **Retrograde Vesicle** continuilly retreive residents enzyme back to earlier
68
What are the three pathway of trans-Golgi network
1. Contistitutive secretion: - Vesicles fuse with the **plasma membrane immediately** - Continuous secretion in all cells 2. Regulated Secretion: - Proteins are packaged into **secretory vesicles** - Vesicles remain stored inside the cell - Fusion with plasma membrane occurs **only upon receiving a signal** 3. Delivery to Lysosomes: - Vesicles move from TGN → **late endosome** - Transport from late endosome → lysosome likely via **direct fusion**
69
# thre List the types of coated vesicles
**1. COPII** - **ER → Golgi** (anterograde) **2. COPI** - **Retrograde:** - Golgi → ER - trans-Golgi → medial-Golgi → cis-Golgi (retrieval) **3. Clathrin** - **Plasma membrane → late endosome** - **TGN → late endosome** *Note:* Coat for TGN → plasma membrane (constitutive/regulated secretion) is **not yet identified**
70
Write the pathway of protein from ER to TGN and their branch pathway
ER → COPII vesicles → cis-Golgi → medial-Golgi → trans-Golgi → TGN ↑ ↓ |—— COPI retrieval ————————| From TGN: 1. Constitutive secretion → plasma membrane 2. Regulated secretion → secretory vesicles → signal-dependent exocytosis 3. Lysosomal pathway → late endosome → lysosome Endocytosis: - Receptor-mediated → early endosome → late endosome → lysosome OR recycling to surface
71
List Four Topological Classes of Integral Membrane Proteins
**Type I** - **Single-pass** - **N-terminus in lumen**, C-terminus in cytosol - Contain: – N-terminal **cleavable signal sequence** – Internal **stop-transfer anchor** = TM α-helix - Signal sequence initiates import → cleaved → stop-transfer halts translocation → TM domain inserted laterally into membrane **Type II** - **Single-pass** - **N-terminus in cytosol**, C-terminus in lumen - Have a single **internal signal-anchor**, not cleaved - Internal signal-anchor: – Acts as ER signal – Acts as membrane anchor - Positively charged residues on **N-terminal side** → keep N-terminus in cytosol ## **Type III** - **Single-pass** - **N-terminus in lumen**, C-terminus in cytosol (opposite of Type II) - Internal signal-anchor near the N-terminus - Signal-anchor also acts as **stop-transfer** - Positively charged residues on **C-terminal side** determine orientation **Type IV (Multipass)** - Multiple TM helices - Two subtypes: **Type IV-A** - **N-terminus in cytosol** - Pattern: – First TM helix = Type II–like internal signal-anchor – Second TM helix = stop-transfer – Subsequent helices alternate signal-anchor and stop-transfer - Examples: GLUT transporters, many ion channels **Type IV-B** - **N-terminus in lumen (exoplasmic space)** - Hydrophobic TM helix near N-terminus + cluster of positive charges → Type III–like orientation - Insertion uses alternating signal-anchor and stop-transfer sequences - Example: GPCRs (7-pass)
72
Explain GPI-Anchored Proteins
73
What is the import machinary of mitochondria
**Matrix-Targeting Sequence** - Location: N-terminus - Length: 20–50 aa - Structure: amphipathic α-helix – One side: positively charged residues – Other side: hydrophobic residues **Import Machinery** **Outer Membrane** - Receptors: **Tom20**, **Tom22** - Channel: **Tom40** **Inner Membrane** - Channel: **Tim23/Tim17** - Import occurs at **contact sites** - Matrix protease cleaves targeting sequence - Final folding often requires chaperonins ## Footnote Tom: Translocon of Outer Membrane Tim: Translocon of Inner Membrane
74
What are requred to import protein into mitochondria genellary
1. Energy 2. Proteins (unfolded) => Cystolic Hsc 70 keeps protein unfolded
75
What binds directly to the NLS on a cargo protein?
Importin α binds directly to the NLS.
76
Which two proteins cooperatively bind a cargo protein to form the trimeric import complex?
Importin α and importin β.
77
Which part of the import complex interacts with NPC components to mediate translocation?
Importin β.
78
What energy source is required for import through the nuclear pore complex?
ATP hydrolysis.
79
What molecule in the nucleoplasm causes dissociation of the import cargo complex?
Ran·GTP.
80
What happens when Ran·GTP binds importin β?
The import cargo complex dissociates and the cargo is released.
81
What protein stimulates conversion of Ran·GTP to Ran·GDP in the cytoplasm?
RanGAP.
82
After Ran·GTP is hydrolyzed to Ran·GDP, what happens to importin β?
It dissociates from Ran·GDP and can initiate another import cycle.
83
Which nuclear factor converts Ran·GDP back to Ran·GTP?
RCC1 (Ran nucleotide-exchange factor).
84
What binds to the NES of a cargo protein to initiate export?
Exportin 1.
85
What molecule binds cooperatively with exportin 1 and the NES during nuclear export?
Ran·GTP.
86
What causes dissociation of the export complex in the cytoplasm?
RanGAP-mediated conversion of Ran·GTP to Ran·GDP.
87
What happens to the NES-containing cargo after export complex dissociation?
It is released freely into the cytosol.
88
Where are exportin 1 and Ran·GDP transported after dissociation in the cytoplasm?
Back into the nucleus through NPCs.
89
Which protein complex binds the 5′ end of mature mRNA to enter the NPC first?
The cap-binding complex (CBC).
90
Why must certain hnRNP proteins be removed during passage through the NPC?
Because they lack NES and would retain mRNA in the nucleus.
91
What allows NES-containing hnRNPs to escort mRNA through NPCs?
They use the exportin 1 + Ran·GTP nuclear export mechanism.
92
What triggers dissociation of shuttling hnRNPs from export receptors in the cytoplasm?
RanGAP-induced hydrolysis of Ran·GTP.
93
After export, what protein binds the 3′ poly(A) tail of mRNA?
Poly(A)-binding protein (PABP).
94
v-SNARE
(vesicle-SNARE) A membrane protein located on the transport vesicle that specifically pairs with a t-SNARE on the target membrane to mediate membrane fusion. ## Footnote on vesicle, fusion
95
t-SNARE
(target-SNARE) A membrane protein located on the target organelle or plasma membrane that binds to the matching v-SNARE, ensuring specific vesicle docking and fusion. ## Footnote on target membrane, recognizes vesicle
96
COP II
(Coat Protein Complex II) A protein coat that drives budding of transport vesicles from the rER to the cis-Golgi — responsible for anterograde transport. ## Footnote ER ➜ Golgi
97
COP-I
(Coat Protein Complex I) A protein coat that mediates retrograde transport — returning proteins and membranes from the Golgi back to the ER, or between Golgi cisternae. ## Footnote Golgi ➜ ER
98
clathrin
A coat protein that forms triskelion-shaped structures, driving vesicle formation involved in endocytosis, and transport from the trans-Golgi network to endosomes and lysosomes. ## Footnote endocytosis & TGN sorting
99
sorting signal
A short, specific amino acid sequence within a protein that directs it to its correct cellular destination by interacting with sorting receptors during vesicular transport. ## Footnote address label (Signal Sequence)
100
WAMP
(Vesicle-Associated Membrane Protein) A major v-SNARE protein found on transport vesicles that pairs with t-SNAREs to drive membrane fusion specificity. (If your slide said “WAMP,” it's almost certainly referring to VAMP.)
101
Quality control in the ER N-linked and O-linked oligosaccharides
A surveillance system in the rough ER that ensures only properly folded and correctly glycosylated proteins proceed to the Golgi. Misfolded proteins are retained, refolded, or degraded through ER-associated degradation (ERAD).
102
N-linked Oligosaccharides
A carbohydrate chain attached to the amide nitrogen of Asn in the consensus sequence Asn-X-Ser/Thr. They are assembled first on dolichol in the ER and play major roles in protein folding and quality control.
103
O-linked Oligosaccharides
Carbohydrate chains attached to the hydroxyl group of Ser or Thr residues. They are added in the Golgi apparatus, usually forming short, linear sugar chains.
104
protein disulfide isomerase
An enzyme in the ER lumen that catalyzes the formation, reduction, and rearrangement of disulfide bonds, allowing newly synthesized proteins to achieve correct tertiary structure.
105
lectin: calnexin,calreticulin
ER-resident lectins that bind monoglucosylated N-linked oligosaccharides on newly made proteins. They retain partially folded proteins in the ER and promote proper folding as part of the calnexin/calreticulin cycle. Calnexin — membrane-bound lectin Calreticulin — soluble ER-luminal lectin Both ensure only correctly folded glycoproteins exit the ER.
106
Tom (the outer membrane translocon)
(Translocase of the Outer Membrane) A protein complex in the outer mitochondrial membrane that recognizes mitochondrial targeting sequences and mediates the initial import of nuclear-encoded mitochondrial proteins.
107
Tim (the inner membrane translocon)
(Translocase of the Inner Membrane) A protein complex in the inner mitochondrial membrane that works with TOM to translocate polypeptides into the mitochondrial matrix or insert them into the inner membrane.