Term
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Definition
| DNA 4 nucleotide code to protein 20 amino acid code |
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Term
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Definition
| DNA 4 nucleotide code to RNA 4 nucleotide code |
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Term
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Definition
[image]
Has anti codon that base pairs with codon and has a 3' OH end that is covalently linked to a amino acyl synthetase enzyme. |
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Term
| What does the endomembrane system consist of? |
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Definition
| Endoplasmic reticulum, the Golgi apparatus, lysosomes, endosomes, and secretory vesicles. |
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Term
| What are the compartments of the endomembrane system used for? |
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Definition
| The processing of proteins for export, proteins destined ro lysosomes, proteins entering the cell. |
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Term
| Do proteins that enter the endoplasmic reticulum ever return to the cytosol? |
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Definition
| No, they are transferred now by vesicles to other compartments of the ER |
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Term
| What are the three major subdivisions of the endomembrane system? |
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Definition
| The secretory pathway, the lysosomal pathway, and the endocrytic pathway. |
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Term
| Can proteins enter in the middle of a pathway? |
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Definition
| No, they must enter at the start. |
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Term
| What is the point of entry into the endomembrane system for a protein destined for the secretory or lysosomal pathway? |
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Definition
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Term
| What is the point of entry into the endomembrane system for a protein destined for endocytosis? |
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Definition
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Term
| Can proteins leave the middle of an endomembrane pathway? |
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Definition
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Term
| Which proteins are processed after translation? |
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Definition
| All (ex. all proteins fold after translation) |
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Term
| What are some events that constitute post translational processing? |
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Definition
| Folding, removal of the first methionine (carried by the start tRNA), methylation, phosphorylation, acetylation, disulfide bridge formation, glycosylation for proteins destined for the cell exterior. |
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Term
| Why does protein folding happen? |
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Definition
| Protein folding is a spontaneous process where the polypeptide takes on the lowest energy conformation. |
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Term
| What proteins help with proper protein folding? |
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Definition
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Term
| What protein deals with misfolded proteins? |
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Definition
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Term
| How does the proteasome work? |
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Definition
| Found in cytosol, degrades proteins that have been tagged with ubiquitin. [image] |
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Term
| What are three types of proteins that enter the endomembrane system upon translation? |
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Definition
1. Proteins destined fro secretion
2. Plasma membrane proteins
3. Proteins that are destined to be endomembrane resident proteins. |
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Term
| What are some characteristics of the endoplasmic reticulum? |
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Definition
1. consists of flattened membrane cistermae and tubules
2. continuous with nuclear envelop
3. may occupy much of the cytoplasmic volume of the cell in synthetically active cells. |
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Term
| What is the rough ER and what is done there? |
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Definition
1. cytosolic surface of the membranes have attached ribosomes that are synthesizing proteins for import into the ER
2. site for synthesis for proteins destined for secretion, lysosomes, and membranes. |
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Term
| What is the smooth ER and what is done there? |
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Definition
continuous with the rough ER
site for lipid and steroid synthesis, makes new membrane |
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Term
| What is the transitional ER and what is done there? |
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Definition
between the rough and smooth ERs
site of vesicle formation and exit of newly synthesized proteins |
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Term
| Which proteins are retained in the ER? |
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Definition
| Proteins that carry an ER retention signal (KDEL or HDEL sequence at their carboxyl ends) |
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Term
| What happens if a protein with KDEL sequence gets out of the ER and enters the cis cisternae of the Golgi? |
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Definition
| Their ER targeting signal gets them sorted into vesicles and moved back to the ER (through trans to cis retrograde movement) |
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Term
| How are abnormal proteins stopped from leaving the ER? |
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Definition
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Term
| What is the unfolded protein response? |
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Definition
| Misfolded proteins in the ER lumen trigger the production of chaperone proteins and the expansion of the ER, promoting proper folding and processing of proteins. [image] |
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Term
| What are key concepts to protein import? |
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Definition
1. each protein contains info in aa sequence that serves as an address.
2. A specific protein receptor corresponds to each type of signal |
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Term
| How do proteins enter the ER? |
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Definition
1. initiation at free ribosomes in the cytosol
2. targeting sequence at hydrophobic end of aa results in the binding of the ribosome to the ER
3. insertion of the polypeptide into ER |
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Term
| What types of proteins are destined for the secretory or lysosomal pathways? |
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Definition
1. proteisn that are completely translocated into the ER (not membrane bound or secreted)
2. proteins that are inserted into membranes |
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Term
| What is the protein that recognizes the Er signal Sequence? |
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Definition
| signal recognition particle |
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Term
| How does the polypeptide enter the ER? Visualization |
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Definition
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Term
| What acts like a translocation channel for the new protein? |
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Definition
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Term
| Why does the rate of translation get reduced when entering the ER? |
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Definition
| Translation stops after SRP attached and restarts after it is unbound (check!) |
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Term
| What types of proteins are inserted into the ER? |
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Definition
1. soluble proteins
2. Membrane proteins |
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Term
| How are soluble proteins entered into the ER? |
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Definition
| Have a single transfer sequence at n terminus that is cleaved off by signal peptidase and then floats freely in ER |
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Term
| What are the two types of start and stop transfer sequences? |
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Definition
1. n terminal signal sequence
2. internal start sequence |
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Term
| What happens if there is a new start sequence? |
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Definition
| The stop sequence before the start sequence detaches the protein from the translocator and the new start sequence attaches onto another translocator. |
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Term
| Is the stop transfer signal ever at the end of a protein? |
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Definition
| No, because then the protein can't elongate into the ER |
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Term
| What is one way we can come up with domain maps? |
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Definition
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Term
| When a vesicle is made, the cytosolic side of the ER remains the cytosolic side of the vesicle (T or F)? |
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Definition
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Term
| Is there a N terminus signal sequence for a single pass membrane protein? |
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Definition
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Term
| Is there a N terminus signal sequence for a double pass membrane protein? |
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Definition
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Term
| What are some ways that scientists can study the endomembrane system experimentally? |
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Definition
1. Visual techniques - microscopy (ex. live imaging with GFP tagged proteins and their movement through cells)
2. Biochemistry
3. Using temperature sensitive mutants |
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Term
| How does autoradiography work? |
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Definition
Frequently used a long time ago
Cover part of a cell with photographic emulsion, specific labelled materials emit beta particles that show up as small grains on the photographic emulsion. |
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Term
| How do you determine the biochemistry of a cell? |
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Definition
1. purify cells
2. Release the cell contents by using mechanical homogenization techniques.
3. Preform cytochemistry techniques to determine biochemistry. |
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Term
| What are some mechanical homogenization techniques that are used to rupture the plasma membrane? |
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Definition
1. High sound frequency
2. mild detergent
3. Small hole
4. shear with rotating plunger |
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Term
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Definition
| Chemical examination that can be detected by microscopic examination |
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Term
| How do you fractionate cell homogenates into their components? |
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Definition
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Term
| How can centrifugation be used to track a protein in transit? |
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Definition
1. continuous labeling experiment (lyse cell at various times, fractionate and look for the fraction with the labelled cell)
2. Pulse and Chase experiment (pulse of radio active specific amino acid then chase with non labelled radioactive amino acid; in order to see which are labelled and which aren't??)
3. Cell fractionation - Sample population at different times after the chase, separate the components of the cell and see how much of the radioactive aa are at each component at different times. |
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Term
| How can you temperature sensitive mutants? |
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Definition
| They can only function within a restrictive temperature and if you take it out of that temperature, they don't work but if you move them back really quickly in to the restricted temperature range, they can work again. |
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Term
| What can does major vesicle transport pathways in eukaryotic cells look like? |
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Definition
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Term
| What are the 5 stages for vesicle transport? |
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Definition
1. Budding
2. Transport
3. Docking
4. Fusion
5. Resetting the system |
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Term
| What are the two methods that budding can be initiated? |
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Definition
1. The cargo pushes up against the membrane
2. Protein coats used to promote membrane curvature |
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Term
| What are the two functions of protein coats? |
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Definition
1. Force membrane to curve and bud
2. Capture cargo molecules for transport |
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Term
| What do the vesicles go with the clathrin and adaptin 1 proteins? |
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Definition
| From the trans golgi network to lysosomes (via endosomes) |
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Term
| What do the vesicles go with the clathrin and adaptin 2 proteins? |
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Definition
| From the plasma membrane to endosomes |
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Term
| What do the vesicles go with the COP proteins? |
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Definition
From ER, Golgi cisterna, or Golgi apparatus to ER, Golgi cisterna, or Golgi apparatus
COPI for Golgi to ER and Plasma membrane
COPII for ER to cis Golgi |
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Term
| map showing the distribution of different types of coat proteins used in vesicle formation in different parts of the endomembrane system |
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Definition
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Term
| What are the steps to vesicle formation? |
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Definition
1. Cargo molecules diffuse around and may bind to receptors (transmembrane protein w/ cargo binding site at lumen side).
2. Adaptin diffuse in cytosol and bind to specific receptors
3. Coat proteins (COP and clathrin) bind to the adaptin that have already bound to the target cells
4. The coating proteins intrinsically help make the curved vesicle shape
5. The newly developed circular shaped membrane has primarily adaptin bound receptors, and not other proteins.
6. Dynamin attach to the neck of the developing vesicle, and driven by GTP hydrolysis, pinches off the vesicle
7. Uncoating starts with the coat proteins and then the adaptin |
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Term
| How can the cell make it so that vesicle contain mainly adaptin bound receptors? |
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Definition
| The coats only have binding sites for adaptin so the concentration of adaptin bound receptors is very high but the concentration of other membrane proteins will be very low because they can't bind to the coat proteins. |
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Term
| How do coat proteins both make the vesicle structure and help determine the concentration of the cargo molecules? |
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Definition
Coat proteins have three arms that each can attach one adaptin. These coat protein trimers then bind to each other and create hexagonal cells
Key idea: the coat proteins are the chief agent to determine the concentration of cargo proteins |
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Term
| What are the two methods of vesicle transport? |
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Definition
Short distance: diffusion
Long distance: move along cytoskeletal tracts (ex. microtubules) and moved by motor proteins like kinesins, dynein, or myosin |
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Term
| What are the steps for vesicle docking? |
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Definition
| Rab proteins (small GTPases) help identify the vesicle as one for that destination (stay on membrane of the vesicle). Then tether proteins bind to the RB vesicle and help bring it in. |
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Term
| What are the different types of SNAREs? |
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Definition
| either named by their location or structure (v-SNAREs, t-SNAREs, or Q-SNAREs, R-SNAREs) |
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Term
| What are the steps for vesicle fusion? |
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Definition
1. SNAREs aid in bringing in the two components close enough so water molecules are pushed out of the way
2. v-SNAREs and t-SNAREs both have to be present
3. For fusion to occur, there must be 1 R-SNARE and 3 Q-SNARES |
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Term
| What is the polarity of the Golgi? |
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Definition
| Vesicles from the ER always enter the Golgi through the cis side and then exit through the trans side |
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Term
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Definition
| The different compartments of the Golgi |
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Term
| How can some proteins move from cis to trans in the golgi and some are resident proteins of the golgi? |
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Definition
1. Vesicle transport model
2. Cisternal Maturation Model
3. Other models |
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Term
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Definition
Cisterna are stationary
vesicles with cargo molecules move from cisterna on the cis side down to the trans side and eventually to the target
If resident proteins accidentally move forward, they get transported back through retrograde vesicle movement |
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Term
| Cisternal Maturation model |
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Definition
cis cisterna move closer and closer to becoming trans cisterna
resident proteins have targetting signals and are transported back via retrograde vesicle movement |
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Term
| Why do vesicles leave the Trans golgi network and where do they go? |
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Definition
1. The maturing lysosome
2. Secretory granules released through regulated secretory pathway
3. Plasma membrane - membrane and proteins released through constitutive secretory pathway |
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Term
| Formation of disulfide bridges |
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Definition
Forms as protein assumes its folded structure
Enzyme protein disulfide isomerase is resident in the ER (as is the enzyme that catalyzes the reaction) because it is unstable in the cytosol (reducing environment) |
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