Lesson 6 Cell Biology

Front 1

Sorting signals

Back 1

Sequences that direct the delivery of a protein to a specific cellular compartment

Front 2

Signal sequences

Back 2

Sorting signals composed of stretches of amino acids 15-60 residues in length

Front 3

Signal Patches

Back 3

Sorting signals composed of multiple internal amino acid sequences that from a three-dimensional arrangement on the surface of a protein

Front 4

Nuclear pore complexes NPC's

Back 4

Arrangement of protein subunits that regulate the gated transport of proteins between the cytosol and the nucleus

Front 5

Nuclear localization signals

Back 5

Sorting signal used to direct large proteins and protein complexes from the cytosol to the nucleus

Front 6

Nuclear import receptors

Back 6

Receptors which bind to NLS and move large proteins into the nucleus through nuclear pores

Front 7

Nuclear export receptors

Back 7

Receptors which bind to nuclear export signals and move large proteins into the cytosol through nuclear pores

Front 8

Ran GTPase

Back 8

GTPase which functions in the regulation of nuclear import and export

Front 9

Cristae

Back 9

Invagination of the mitochondrial inner membrane

Front 10

Post-translational translocation

Back 10

The import into an organelle of proteins translated in the cytosol

Front 11

Protein translocators

Back 11

Multiprotein complexes which mediate the translocation of proteins across membranes

Front 12

TOM complex

Back 12

involved in the translocation of all nuclear-encoded mitochondrial proteins. (Mitochondrial outer membrane protein translocator)

Front 13

TIM complex

Back 13

Inner membrane complexes that transport soluble proteins into the matrix space and assist in the insertion of
proteins into the inner membrane. (Mitochondrial inner membrane protein translocator)

Front 14

SAM complex

Back 14

Mitochondrial outer membrane complex involved in the folding of B-barrel porin proteins (sam & tom)

Along with OXA complex mediate the insert of proteins into mitochondrial membranes.

Front 15

OXA complex

Back 15

Mitochondrial inner membrane complex involved in the insertion of inner membrane proteins (oxa & tim)

Along with SAM complex mediate the insert of proteins into mitochondrial membranes.

Front 16

Chaperone proteins

Back 16

Proteins which bind to other proteins and help them into the properly folded structure

Front 17

Mitochondrial Hsp70

Back 17

Part of the TIM translocator. This protein binds to imported proteins as they emerge from the TIM channel and help to ‘pull’ the protein into the matrix space using the energy from ATP hydrolysis

Front 18

Stop transfer signal

Back 18

Hydrophobic sequence that halts the translocation of a polypeptide chain through a membrane

Front 19

Co-translational translocation

Back 19

The import of protein into an organelle before translation is complete

Front 20

Signal-recognition particle (SRP)

Back 20

Complex which binds to an ER signal sequence as it emerges from the ribosome, halts further translation and binds to receptors on the ER membrane

Front 21

Sec61 complex

Back 21

Complexes which form ER protein translocators

Front 22

ER signal peptidases

Back 22

Cleave ER signal sequences to release proteins into the cisternae

Front 23

ER retention sequence

Back 23

Four amino acid sequence at the C-terminal of a protein which prevent its translocation to another organelle

Front 24

N-linked oligosaccharide

Back 24

Oligosaccharides covalently linked to asparagine residues of proteins

Front 25

Oligosaccharyl transferase

Back 25

ER translocator-associated enzyme that transfers a precursor oligosaccharide to certain asparagine residues on proteins imported into the ER

Front 26

Calnexin, calreticulin and BiP

Back 26

3 ER chaperone proteins involved in mediating proper protein folding

Front 27

Unfolded protein response

Back 27

Increased transcription of protein involved in retrotranslocation and cytosolic protein degradation due to accumulation of unfolded proteins in the ER

Front 28

Scramblase

Back 28

Enzyme which catalyzes the transfer of newly formed lipids to the lumenal leaflet of the ER membrane

Front 29

Flippases

Back 29

Plasma membrane enzymes which catalyze the transfer of specific phospholipids from the extracellular leaflet to the cytosolic leaflet

Front 30

Retrotranslocation or dislocation

Back 30

Translocation of misfolded ER proteins back to the cytosol for degradation

Front 31

Proteasomes

Back 31

Cytosolic structure where ubiguitylated proteins are degraded

Front 32

Rough ER

Back 32

Has ribosome bound to its cytosolic face

Front 33

Smooth ER & Rough ER(functions) 4

Back 33

1.Synthesis of soluble and intregral membrane proteins
2. most proteins made in the RER are secreted outside the cell or transported other organelles
3. synthesis of most lipids
4. Storage of Ca+

Front 34

Golgi Apparatus

Back 34

1. stacks of disc-like compartments called cisternae
2. Modify proteins and lipids received from the ER and transfers them to various cellular location

Front 35

Mitochondria (and chloroplasts in plants)

Back 35

generate ATP, have their own DNA
Mitochondria function in the
synthesis of ATP using energy derived from electron transport and oxidative
phosphorylation.

Front 36

Lysosomes

Back 36

1. contain digestive enzymes
2. degrade intracellular organelles and macromolecules from inside and outside of the cell

Front 37

Endosomes

Back 37

Transport extracellular molecules (taken up by endocytosis) to lysosomes

Front 38

Peroxisomes (3 functions)

Back 38

contain enzyes used in oxidation reactions

Along with mitochondria, peroxisomes are a major site of oxygen utilization. Peroxisomes enzymes carry out a variety of functions such as: (1) use of
molecular oxygen to remove hydrogen atoms from organic substrates (carried out by an
oxidases), (2) use of H2O2 to oxidase substrates and the removal of excess H2O2 (carried
out by catalases), and (3) breakdown of fatty acids by process of β-oxidation.

Front 39

Gated Transport

Back 39

a. movement of proteins between cytosol and nucleus
b. nuclear pore complexes act as selective gates which transport specific macromolecules (containing the apropriate sorting signal)
c. Also allow for diffusion of small molecules

Front 40

Transmembrane transport (protein translocation)

Back 40

a. movement between cytosol and mitochondria/chloroplast, peroxisiomes, ER
b. transmembrane protein translocators recognize sorting signal and directly transport specific proteins across a membrane from cytosol to lumen of an organelle
c. translocated protein usually must unfold to pass through the translocater

Front 41

Vesicular transport

Back 41

a. Secretory and endocytic pathways
b. transposrted proteins do not need to pass through a membrane
c. cargo-loaded membrane vesicles pinch off from a compartment (donor) and fuse with another compartment (target) and unload cargo
d. Used to move cargo between topologically equivalent compartments
e. the membrane orientation is preserved between donor and target, with the same monolayer facing the cytosol

Front 42

Nuclear Envelope

Back 42

double membrane surrounding the nucleus. Consists of an outer and inner membrane and is perforated by nuclear pores

Front 43

Nuclear envelope inner membrane

Back 43

contains anchoring sites for chromatin and the nuclear lamina (a structurally supporting protein network)

Front 44

Nucl. Env. Outer Membrane

Back 44

1. Continuous with ER
2. Displays ribosomes and carries out protein synthesis
3. Newly formed proteins enter into perinuclear space, which is continuous with the lumen of the ER

Front 45

Nuclear Lamina

Back 45

located on the nuclear side of the inner membrane
1. made of up of nuclear lamins: meshwork of interconnected intermediate filament proteins
2. gives shape and stability to NE
3. Anchored to the nuclear envelope at the NPC and by integral membrane
proteins in the inner membrane
4. Chromatin interacts with both the nuclear lamina and inner membrane
proteins

Front 46

Transport: Cytosol to nucleus

Back 46

occurs via nuclear pores
-histones, DNA & RNA polymerases, gene regulatory proteins, RNA processing proteins

Front 47

Transport: Nucleus to cytosol

Back 47

occurs via nuclear pors which span the nuclear env
-tRNAs, mRNAs

Front 48

GTPase-activating protein (GAP) 5 items

Back 48

1. a RAN specific reg prot
2. located in cytosol
3. triggers GTP hydrolysis
4. converts Ran-GTP to Ran-GDP
5. Ran-GDP is transported into the nucleus by its own import receptor which is specific for the GDP-bound conformation

Front 49

GEF. Guanine Exchange Factor

Back 49

1. Ran-specific regulatory
protein
2.Binds to chromatin in nucleus
3. Promotes exchange of GDP for GTP
4. Converts Ran-GDP to Ran-GTP

Front 50

Which Ran-specific regulatory
protein is found mostly in the nucleus?

Back 50

Ran-GTP

Front 51

Which Ran-specific regulatory
protein is found mostly in the cytosol?

Back 51

Ran-GDP

Front 52

The cycle of binding of Ran-GTP to import receptors promotes cargo release in the
nucleus... list steps (5)

Back 52

a. When cargo-import receptor complexes arrive in nucleus, Ran-GTP binds and
the cargo is released.
b. Ran-GTP-receptor complex is transported back to cytosol
c. In cytosol, GEF converts Ran-GTP to Ran-GDP
d. Ran-GDP is released by the receptor
e. Receptor is ready to bind new cargo

Front 53

The cycle of binding of Ran-GTP to export receptors promotes cargo binding in the nucleus ... list steps (3)

Back 53

a. When cargo-export receptor complexes arrive in cytosol, GAP hydrolyzes the
GTP and converts Ran-GTP to Ran-GDP
b. Export receptor releases it cargo and Ran-GDP
c. Export receptor returns to the nucleus

Front 54

Breakdown and reassembly of nuclear envelope during mitosis

Back 54

During mitosis, the nuclear envelope breaks down, dispersing many nuclear proteins into
the cytosol. After the nuclear envelope reforms, these protein need to be re-imported into
the nucleus.

Front 55

Endoplasmic Reticulum
description

Back 55

is a branching network of interconnected tubules and
flattened sacs that extends throughout the cytosol.

The ER has two distinct regions, rough
endoplasmic reticulum (RER) with bound ribosomes, and SER lacking ribosomes

Front 56

Rough ER (3)

Back 56

is the site for the production of soluble and membrane proteins for most
cellular organelles and the plasma membrane.

Water-soluble proteins destine for lumens of
organelles, or secretion into extracellular space, are completely translocated across the ER
membrane into the ER lumen.

Proteins destine for organelle or plasma membranes are
only partially translocated and become embedded in ER membrane.

Import of most
proteins into the ER is co-translational

Front 57

Assembly of lipid bilayers (3)

Back 57

occurs in the cytosolic leaflet of the ER membrane.

Some newly formed lipids are transferred to the lumenal leaflet of the ER by a phospholipid translocater
called scramblase, resulting in an equal distribution of the different types of phospholipids
between the two leaflets of the ER membrane.

In the plasma membrane, flippases
specifically remove phospholipids with free amino groups in their head groups
(phosphatidylserine and phosphatidylethanolamine) from the extracellular leaflet to the cytosolic leaflet, resulting in an asymmetric phospholipid composition

Front 58

Smooth ER (3)

Back 58

SER participates in the synthesis of steroid hormones,
the detoxification of lipid-soluble drugs and the storage of Ca2

Front 59

Protein folding...summary (4)

Back 59

1. Only properly folded proteins, and proteins that assemble normally, are allowed to leave the ER lumen and translocate to other organelles.

2. Unfolded proteins are bound by ER chaperone proteins (calnexin, calreticulin, BiP) until they fold correctly.

3. Proteins which do
not properly fold in the ER are retrotranslocated or dislocated back to the cytosol where
they are destroyed in proteasomes.

4. If misfolded proteins start to accumulate, the unfolded
protein response is triggered, resulting in increased transcription of proteins involved in
retrotranslocation and protein degradation in the cytosol.

Front 60

Glycosylation of synthesized ER proteins...? (5) general info, probably not worth too much time.

Back 60

1. Most protein synthesized in the ER are glycosylated by the transfer of a precursor
oligosaccharide from a dolichol membrane lipid (where it is assembled) to certain asparagine residues (N-linked glycosylation).

2. Transfer is carried out by a membranebound,translocator-associated oligosaccharyl transferase.

3. Oligosaccharides are later modified in the ER and the Golgi apparatus, resulting in a large diversity of N-linked
oligosaccharides on mature glycoproteins.

4. N-linked oligosaccharides are the most common oligosaccharides, comprising 90% of all glycoproteins.

5. Very few cytosolic proteins
are glycoproteins, and those that are have only a single sugar residue attached.

5. ER enzymes also covalently attach a glycosylphosphatidyl-inositol (GPI) anchor to the Cterminus of some membrane proteins destined for the plasma membrane

Front 61

Proteins directed to the ER. 6 Steps

Back 61

1. Proteins are directed to the ER by an ER signal sequence, which are bound by signal recognition particles (SRPs) as they emerge from the ribosome exit site.

2. A translation pause domain of the SRP stops translation, giving the SRP-bound ribosome time to bind to
a SRP receptor on the ER membrane.

3. The SRP-ribosome complex is brought to a protein
translocator in the ER membrane

4. the SRP and SRP receptor are released,

5. the signal
sequence binds to the translocator,

6. translation restarts and the growing peptide passes
across the ER membrane.

Front 62

Lumenal proteins 3 steps

Back 62

For lumenal proteins, the signal sequence is cleaved and the
protein is released into the lumen.

Front 63

Membrane proteins 3 steps

Back 63

Membrane proteins have a series of start- and stoptransfer
sequences.

1. As each stop-transfer sequence enters the translocator pore,
translation stops

2. the translocator opens laterally and

3. the protein moves out into the lipid bilayer.

Front 64

T/F
ER signal sequences are both necessary and sufficient to direct a protein to the endoplasmic reticulum

Back 64

true

Front 65

T/F
Only proteins released into the lumen are glycosylated in the ER.

Back 65

False

Front 66

T/F
The ER membrane is continuous with the inner membrane of the nuclear envelope

Back 66

False

Front 67

T/F
Proteins must be unfolded to pass through mitochondrial translocators.

Back 67

true

Front 68

A co-translational translocation mechanism is used to import proteins into the ______________.

Back 68

RER

Front 69

The perinuclear space is continuous with ______________________.

Back 69

lumen of the ER

Front 70

Organelle where β-oxidation of fatty acids occurs.

Back 70

peroxisomes

Front 71

The TOM complex is required for the translocation of all nuclear-encoded proteins into the ____________.

Back 71

mitochondria

Front 72

When proteins are glycosylated in the ER, the oligosaccharide is covalently linked to what amino acid residue?

Back 72

asparagine