Mtc: Jan 13 Part 3-Er, Golgi Apparatus, Protein Processing, Targeting, Etc

Front 1

A _____ is the smallest unit of biological autonomy/

Back 1

Cell

Front 2

Microscopically, the _____ _____ appears to represent the boundary where the genetic program of a cell interacts with the environment in which the cell resides

Back 2

-Plasma Membrane

Front 3

Function of Smooth ER

Back 3

-Involved in mobilization of glucose from glycogen
-Storage depot of intracellular Ca++
-Many cytochrome P450 enzymes located in the SER=serves as the site for lipid synthesis and drug detoxification

Front 4

Function of Rough ER

Back 4

-Location where secretory and membrane proteins first pass through or enter a membrane
-With ribosomes serves in the 1st stage of protein sorting
-Other: Glycosylation, folding, quality control and degradation

Front 5

Golgi

Back 5

-4 -7 closed slightly cupped "pita-configured" membranes

Front 6

What are the 3 types of end secretions of from the Golgi?

Back 6

-Lysosome
-Plasma Membrane
-Secretory Vesicle

Front 7

Transport Vesicles (Golgi); What is the name of the mechanism of transport?

Back 7

-Vesicles that appear to be mediating the flow of membranes--and proteins embedded in or contained in the lumen---from one cellular compartment to another
-Vesicular transport

Front 8

Anterograde vesicular transport

Back 8

-The movement of membrane and luminal material from the ER, through the transport vesicles to the plasma membrane
-Mjr pathway for protein secretion, as well as in delivering cell surface proteins to the plasma membrane

Front 9

Retrograde Vesicular transport

Back 9

-The movement of membrane material in the opposite direction of anterograde vesicular transport

Front 10

What 2 organelles do not participate in the membrane trafficking?

Back 10

-Mitochondria
-Peroxisomes

Front 11

What percentage of proteins synthesized remains in the cytoplasm?

Back 11

30-50%

Front 12

In order for proteins to function correctly, what needs to happen?

Back 12

Must be folded correctly

Front 13

Chaperones

Back 13

-Class of proteins that catalyzes the correct folding of proteins

Front 14

Chaperone-assisted protein is generally an ____ ___ ___.

Back 14

Energy requiring process

Front 15

In order to accurately sort and deliver a protein into the appropriate cellular compartment(s), a _____ ____ on the protein molecules needs to be recognized. This can be part of a ___ ___ of the protein or a moiety that is added on after ____.

Back 15

-Sorting Signal
-Coded sequence
-Translation

Front 16

Secretory Pathway

Back 16

A major pathway delivery that involves the DR and Golgi from which proteins may be exported from the cell through the vesicular transport system

Front 17

A shared feature of organelle-trageting pathways is the use of a _____ ____ intrinsic to the proteins destined for these organelles which in turn have membrane-bound receptors for the this.

Back 17

Signal Sequence

Front 18

What happens to proteins that don't have a signal sequence?

Back 18

Remain in cytoplasm

Front 19

Nuclear proteins are distinguished from non-nuclear proteins by having a peptide domain called _____ ______

Back 19

Nuclear localizing signal (NLS)

Front 20

Proteins with an NLS are complexed with specific transport proteins called _____ and translocated into the nucleus through the center of the NPC.

Back 20

Importin

Front 21

Distinct Differences for nuclear export of proteins, tRNA, ribosomal subunits many other ribonucleoproteins (RNPs)

Back 21

-Nuclear-export signal (NES) in the "cargo" protein that complexes with a carrier called exportin

Front 22

mRNP exporter

Back 22

-Most newly mRNAs are exported through this mechanism through the nuclear pores
-After nuclear export, the protein subunits of the mRNP exporter are re-imported into the nucleus using the importin-mediated pathway

Front 23

What does the physical localization of ribosomes onto the rough ER help with?

Back 23

Transport of the nascent peptide into the ER lumen

Front 24

Cotranslation translocation

Back 24

-Transport of secretory proteins into the ER lumen as it is being translated

Front 25

ER signal sequence

Back 25

-N-terminal of all secretory proteins consists of this 16 to 30-residue amino acid sequence

Front 26

What cytoplasmic protein is the 1st molecule to recognize and bind to the N-terminal signal sequence?

Back 26

Signal Recognition Particle (SRP)

Front 27

Signal Recognition Particle (SRP)

Back 27

-cytoplasmic protein that is the 1st molecule to recognize and bind to the N-terminal signal sequence
-Attaches to the ER membrane via SRP receptors (binding facilitated by GTP)

Front 28

What occurs with the SRP (signal recognition particle)?

Back 28

-Hydrolysis of GTP bound to SRP
-SRP receptor then occurs=the disassembly of the SRP-SRP receptor complex
-Followed by insertion of the peptide into an adjacent transmembrane channel (the translocon channel)
-GDP is released from both the SRP and SRP receptor

Front 29

Translocon: Where is it inserted?

Back 29

-Insertion of peptide into an adjacent transmembrane channel

Front 30

What cleaves the entire signal sequences after it has entered the ER lumen?

Back 30

Signal Peptidase

Front 31

2 Major Covalent Modifications in the RER that Secretory and Membrane proteins usually go through

Back 31

-Glycosylation
-Disulfide bonds formation

Front 32

Glycoproteins

Back 32

Proteins that are tagged with oligosaccharide side chains (Protein is the main component)

Front 33

Protein Glycosylation

Back 33

Process of covalently attaching oligosaccharide side-chains to proteins which occurs post-translationally

Front 34

What % of proteins are glycosolated?

Back 34

20%

Front 35

Proteoglycans

Back 35

Macromolecules consisting of heteropolysaccharides (glycan) joined to a polypeptide (polysaccharides are the main compenent)

Front 36

Glycosylation

Back 36

-Dynamic Process that is closely regulated
-Glycosyltransferense gene are expressed in a tissue-specific manner under temporal control

Front 37

Glycosyltransferase

Back 37

Enzymes that carries out glycosylation

Front 38

Polysialic acid

Back 38

Important for modulating the adhesive properties of cells during neural innervation and migration of axonal processes

Front 39

What does glycosylation have a profound effect on? Why?

Back 39

-Proteins structure
-Forces protein backbones into an extended conformation

Front 40

_______ groups on proteins can mediate protein-protein binding.

Back 40

Carbohydrate

Front 41

Significant Effects Glycosylation of Serum Proteins on Half-lives

Back 41

-Sugar tags increase the mass of small protein hormones and reduce hormone loss by kidney filtration
-Carbs side chains provide resistance to proteolysis and immune detection
-Hepatocyte macrophage receptors bind to specific carbohydrate side chains and clear glycoproteins from plasma

Front 42

What gives great diversity of linear and branched sugar structures?

Back 42

-Variable linkage flexibility of glycan chain

Front 43

Glycotransferase

Back 43

-Enzyme in the ER or Golgi that catalyzes the covalent transfer of monosaccharide or oligosaccharide units to the proteins to be glycosylated

Front 44

2 Major Types of Protein Glycosylation

Back 44

-N-glycosylation
-O-gylcosylation

Front 45

N-glycosylation

Back 45

-Sugar peptide linkage is through the nitrogen atom of an asparagine (Asn) residue

Front 46

N-linked glycan

Back 46

-N-linked oligosaccharide that consists of a core of pentasaccharide---2 N acetylglucosamine and 3 mannose molecules---attached to the nitrogen atom of asparagine's R-group

Front 47

O-Glycosylation

Back 47

When a glycan chain is linked to an amino acid side chain through the oxygen atom of the R-groups of serine or threonine it forms this
-->simpler in structure compare to N-linked gylcans

Front 48

5 Types of O-Glycans

Back 48

-Mucin-type
-Proteoglycan
-EFG repeat
-Collagen
-Dystroglycan

Front 49

How does the glycosylation of proteins in the RER occur?

Back 49

-Cotranlationally

Front 50

Rather than building the glycan chain in situ on the peptide one sugar residue at a time, a preformed glycan structure is transferred wholesale onto the peptide at the apporpriate _______ residue.

Back 50

Aspargine

Front 51

The preformed oligosaccharide is constructed in a stepwise manner beginning with a membrane anchor molecule called ____ ____ on the cytoplasmic surface of the ER.

Back 51

-Dolichol phosphate

Front 52

Oligosaccharyl Transferase

Back 52

catalyzes a 14-residue oligosaccharide is transfeered to the appropriate aspargine residues on the nascent peptide when exposed in the ER lumen

Front 53

How are intermolecular and intramolecular disulfide bonds formed? What is this reaction catalyzed by?

Back 53

-By the condensation of sulfhydral groups from 2 amino acids (most often cysteine)
-Protein disulfide isomerase (present in RER)

Front 54

3 Different Classes of Chaperones

Back 54

-Shield hydrophobic regions of growing peptide and help fold these regions into the interior of the final protein molecule
-Intramolecular disulphide bind formation almost always constrains the structure of the molecule
-Proofreading or quality control function (recognize proteins with glycan chains that have one terminal glucose residue)

Front 55

What happens after proteins emerge from the translocon?

Back 55

-Chaperones (such as BiP) help fold the peptide
-N-glycosylation takes place at the same time
--->When the synthesis is complete the protein is released and glucosidases I and II remove the 1st 2 terminal glucose residues, respectively

Front 56

Once a protein is released, what removes the 1st 2 terminal glucose residues during protein folding? What takes over after this?

Back 56

-Glucosidases I and II
-Chaperone such as calnexin and calreticulin, because of their affinity for glycoproteins with glycans containing terminal glucose, takes over.

Front 57

What 2 chaperones have an affinity for glycoproteins with glycans containing a single terminal glucose?

Back 57

Calnexin and Calreticulin

Front 58

What do chaperones do in protein folding?

Back 58

-Proofreading chaperone (calnexin) binds to the single glucose residue in the presence of a disulfide isomerase and disulfide bond formation will also occur
-When these chaperones are finished, the remaining glucose residue will be removed by glucosidase II, and the protein is released and ready to move onto to its next stations such as the Golgi for a secretory protein

Front 59

What happens when a protein is folded incorrectly? What is the name of this mechanism

Back 59

-Unfolded and misfolded proteins are the substrates of another glucosyltransferase that adds back a terminal glucose residue
-Such a protein will be subject to another round of chaperone action by calnexin and ERp57
-If proper folding finally occurs, quality control in protein production is achieved

-->Surveillance or Quality Control Mechanism

Front 60

The ____ serves a s a sensor for misfolded proteins.

Back 60

Glucosyltransferase

Front 61

Why are unfolded and badly folded proteins that are recalcitrant to be properly folded a significant problem for the cell?

Back 61

-Quite likely, the exposed hydrophobic domains of the misfolded proteins results in protein aggregation, which can disrupt chaperone activities for other proteins=creates significant cellular crisis referred to as ER stress

Front 62

ER Stress

Back 62

significant Cellular crisis
-->could be because of unfolded and badly folded proteins that form aggregates

Front 63

2 Pathways that Have Been Evolved to Deal with ER Stress

Back 63

-ER associated degradation (ERAD)
-Unfolded Protein Response (UPR)

Front 64

ERAD

Back 64

-ER-associated degradation
-UNfolded proteins are exported to the cytosol (through an as yet unknown mechanism) for rapid degradation by the proteosome using a ubiquitin-mediated pathway

Front 65

UPR

Back 65

-Unfolded protein response
-Response program triggered by unfolded protein acuumulation in the lumen that is mult-tiered
-Results in the attenuation of protein synthesis and causes cell cycle arrest, as well as up-regulates the production of chaperones, RER and protein secretion machinery
-The goal is to decrease the level of proteins in the ER lumen

Front 66

What is the goal of UPR

Back 66

To decrease the level of proteins in the ER lumen

Front 67

___ ____, _____ and _____ are clinically very significant because a large number of genetic disorders is caused by mutations that result in protein misfolding.

Back 67

ER Stress, ERAD, and UPR

Front 68

Peptides destined to be an integral membrane proteins falls into 5 Topological Catergories

Back 68

Type I to IV

Front 69

Type I membrane proteins

Back 69

Initially translated and transported into the ER lumen as in secretory proteins, with continued translation after the signal sequence has been cleaved
-However, Type I membrane proteins have a peptide sequence , called the stop-transfer anchor that is highly hydrophonic

Front 70

Functions of Stop-transfer anchor sequence (Type I membrane proteins)

Back 70

-It stops continued translation of the peptide while the sequence is in the translocon
-It serves as the transmembrane hydrophobic domain of the resulting membrane protein after the peptide has been moved laterally into the ER membrane

Front 71

Where are the Type I membrane proteins in the signal sequences located? What does this allow?

Back 71

-NOT in N-terminus
-Internal region of the peptide-->allows for a more complex sequence o topological events resulting in the different orientations of the N- and C-terminal with respect to the extracellular or cytoplasmic space, and to the number of passes of the peptide through the membrane

Front 72

Where are proteins that are secretory from the cell or destined to function in the lysosomes or on the cell surface transported by?

Back 72

Secretory Pathway

Front 73

What are all protein trafficking in the secretory pathway mediated by? What do they carry?

Back 73

Transport vesicles which carries "cargo proteins" that bud form a donor compartment and fused with a target compartment

Front 74

The first phase of the secretory pathway takes place in the ______, where proteins are ______ and passed into the lumen, properly modified and folded.

Back 74

-RER
-Synthesized

Front 75

Where does anterograde transport carry proteins after leaving the ER?

Back 75

CGN

Front 76

Cisternal Maturation

Back 76

CGN progressed through a "maturation" process through which they ultimately become TGN, while the protein cargo within its lumen became progressively modified to its final form

Front 77

What occurs as the cisternae are going through maturation?

Back 77

Retrograde transport vesicles are also formed that deliver cargo proteins from the more distal cisternae to the more proximal cisternae

Front 78

At TGN, transport vesicles carry secretory protein to the ____ ___, lysosomal proteins to the _____.

Back 78

-Cell Surface
-Lysosomes

Front 79

Formation of transport Vehicles

Back 79

-Recruitment of specific soluble GTP-binding coat proteins (e.g. clathrin) from the cytosol to in a small patch of membrane from the donor compartment
--->Patch of membrane contains cargo protein, receptor fo soluble proteins, and protein v-SNARE

Front 80

The recruited coat proteins generally have receptors for the ____ ___ of the membrane cargo proteins and/or receptors for _____ ____ such that the coat proteins forms a ____ with these receptors.

Back 80

-Cytoplasmic Domain
-Soluble proteins
-Complex

Front 81

What does aggregation of the coat protein with each other result in?

Back 81

-Curvature of the membrane, creating a "pit"-like structure that eventually buds off to become a transport vesicle

Front 82

What happens to the coat proteins after budding occurs?

Back 82

-The coat protein is shed (with hydrolysis of GTP), leaving vesicles with exposed v-SNARE molecules that interact with similar molecules (t-SNARE) on the target membrane mediates the fusion of transport vehicles with the target membrane compartment
-Fusion with the plasma membrane results in the secretion of the cargo soluble proteins being secreted into the extracellular space

Front 83

What do coat proteins require in order to bind to the cargo protein receptors?

Back 83

-Adapter protein (AP) complex

Front 84

What is needed for the budding of the vesicles?

Back 84

-Dynamin

Front 85

Many membrane and secretory proteins require ____ _____ of a _____ as a part of their processing. Give an example

Back 85

-Proteolytic Cleavage
-Proprotein
-Insulin: synthesized as a larger molecule called proinsulin

Front 86

The same mechanism that lead to the formation of transport vesicles from the membrane of the ER or Golgi apparatus can occur at the ____ ____, the resulting vesicles will contain material from the _______ _____.

Back 86

-Plasma Membrane
-Extracellular space
-->Process called endocytosis

Front 87

Pinocytosis

Back 87

content taken up is a small droplet of extracellular fluid

Front 88

Phagocytosis

Back 88

foreign material taken up via the plasma membrane (resulting vessel called phagosome)

Front 89

If specific ligand molecules are taken up by binding to specific ligand receptors followed by endocytosis, it is called ___ ___ ____, and the resulting vesicle is called an ____ _____, which will "mature" to form a ____ ____.

Back 89

-Receptor Mediated Endocytosis
-Early Endosome
-Late Endosome

Front 90

LDL uptake begins with the recognition of the ______ by a cell surface receptor, the ____ ____, which results in endocytosis through a ___ ___ ____.

Back 90

-apoB
-LDL receptor (LDLR)
-clathrin-mediated pathway

Front 91

What is critical to the interaction of LDLR and the AC complex?

Back 91

-Recognition sequence on the LDLR, referred to as the NPXY sequence (asparagines--proline--any amino acid---tyrosine)

Front 92

What occurs after the coated vesicle is formed using a dynamin-mediated mechanism?

Back 92

-The clathrin coat is shed and early endosome is formed
-The early endosome fuses with the late endosome and the low pH within the latter causes a change in conformation of the LDLR and consequently the LDL particle is released

Front 93

How is the LDLR recycled to the plasma membrane they will regain their LDL binding conformation? What happens to the remaining late endosome?

Back 93

-Through vesicular transport
-Remaining late endosome fuses with a lysosome where the LDL s broken down to its constituent parts

Front 94

What is vital importance for the regulation of cholesterol synthesis?

Back 94

-Intracellular cholesterol generated in the vesicular transport pathway

Front 95

What can mutations in the gene for LDLR or ApoB lead to?

Back 95

Signficant defect in the regulatory pathway of vesicular transport

Front 96

Autophagy

Back 96

When cells are stressed (e.g. starvation), they are generally triggered to initiate a cascade of events that include recycling of macromolecules
-This can be done by breaking down existing cell structures

--->Such recycling is called autophagy

Front 97

Autophagosomes

Back 97

-Double membraned Vesicles that are formed by autophagy

Front 98

What does the outer membrane of a autophagosome contain that facilitates its fusion with lysosomes? What happens to the autphagosome after this?

Back 98

-Proteins
-Reduced to a single-membraned structure

Front 99

What are potent inhibitors of autophagy?

Back 99

Amino Acids

Front 100

Where is the primary cellular location for proteolysis?

Back 100

Lysosome

Front 101

Proteosomes

Back 101

-Second most important cellular compartment for proteolysis
-Abundant in the cell
-Cylindrically-shaped protein complex that has a cap and a hollow core, the later of which forms the proteolytic chamber of the proteosome

Front 102

What are the protein subunits of proteosome complex?

Back 102

Alpha and Beta types

Front 103

What is the function of alpha type subunits? (Proteosome)

Back 103

-To propel proteins to be degraded through the core

Front 104

What is the function of the beta type subunits? (Proteosome)

Back 104

-Provide with proteolytic function
-Enzyme activity: trypsin-like, chymotrypsin-like, caspase-like activities

Front 105

The proteosomes are an important compartment for regulated _____ ____.

Back 105

Protein degradation

Front 106

What are targets of proteosomal degradation?

Back 106

-Unfolded and misfolded proteins
-Regulatory proteins especially those of the cell cycle
-Transcriptional regulators of key proteins in signal transduction pathways

Front 107

What do proteosomes play a vital role in?

Back 107

-Developmental regulation and cell cycle control

Front 108

Proteosomal protein degradation is an integral component of _____.

Back 108

ERAD

Front 109

What is the key of regulating proteolysis by the proteosomes?

Back 109

-Conjugation of multiple copies of a peptide called ubiquitin to the protein that is degraded

Front 110

Ubiquitin

Back 110

-76 amino acid protein with the C-terminal glycine residue capable of forming an isopeptide bond with a side chain of lysine on a target protein

Front 111

What does ubiquitin need in order to conjugate to a protein to be degraded?

Back 111

-Participation of a ubiquitin-activating enzyme (E1)
-Ubiquitin-conjugating enzyme (E2)
-Ubiquitin Ligase (E3)

Front 112

Additional ubiquitin molecules are added onto the 1st ubiquitin molecule by a yet unknown pathway to yield a ___ ___.

Back 112

Polyubiquitinated protein

Front 113

Humans have ___ E3 enzymes, a _____ set of E3 enzymes and an even ____ set of E1 enzymes.

Back 113

~500
-Small
-Smaller

Front 114

Usually polyubiquitn with __ to ___ subunits is sufficient to target the protein to be degraded to the proteosome.

Back 114

4 to 5

Front 115

The ___ de-ubiquitinates the target protein molecule as it is being fed through the proteolytic chamber of the proteosomal core, and the ubiquitin is _____. What happens to the protein?

Back 115

-Cap
-Recycled
-Cleaved into short peptides