Exam II: Chapter 15 and Extras

Chapter 15 + details from ppt

nuclear pore

bidirectional channel with meshy cage throughout hole

* passive transport
* an actual gap in the membrane

nuclear localization signal

positive string of amino acids that signal for the nucleus

* anywhere in amino acid order

cargo protein

the functional protein that is being moved

bidirectional channel

allows passive movement of solutes both ways

cytosolic fibril

grab protein with NLS and importin attached on cytosolic side to stuff them through nuclear pore

alpha importin

beta importin

importin

grab nucleus proteins based on NLS and transport to nucleus

* transport receptors

Ran-GTP

binds to importin to release cargo

* high concentration in the nucleus
* functional protein

exportin

takes substrate out of the nucleus to cytosol

* transport receptors

guanine exchange factor

replaces the GDP on Ran-GDP

Ran-GDP

non-functional importin

* high concentration in cytosol

nuclear transport

1. proteins made on free ribosome
2. importin grabs folded protein
3. cytosolic fibril push protein through mesh
4. Ran-GTP binds
5. cargo released from importin
6. Ran-GTP (exportin) takes importin to cytosol

6a) pushed out by nuclear fibril?


7. GTP hydrolysis
8. Ran-GDP releases importin


1. GEF replaces GDP on Ran-GDP to become Ran-GTP

mitochondria

made of an outer membrane, inner membrane, inner membrane space, and matrix

CHSP70

stabilizes unwound proteins destined for mitochondria

mitochondrial signal sequence

positive amino acids that say “take me to the mitochondria”

* at N terminus

receptor protein

click into mitochondrial protein from cytosolic side

TOM

translocator that helps push mitochondrial protein through outer membrane with chaperones

TIM

translator that helps push mitochondrial protein through inner membrane with chaperones

HSP60

prevent mitochondrial protein from folding when going through TIM and TOM

HSP70

help fold mitochondrial protein

secondary sequence

tell final destination within an organelle

inner membrane space

more positive region of mitochondria

chloroplast signal sequence

positive amino acids that say “take me to the chloroplast”

TOC

chloroplast outer membrane translocator

TIC

chloroplast inner membrane translocator

peroxisome

self replicating organelle

proteins delivered folded

Functions:

* oxidative reactions
* has catalase and crate oxidase
* takes protons off organics
* detoxifies ethanol
* breaks down fatty acids

peroxisome signal sequence

string of positive amino acids that say “take me to the peroxisome”

* at **C terminus**

endomembrane system

protein delivery system

1) bound ribosome

2) ER

3) Golgi apparatus

4) plasma membrane, secretion, lysosome

co-translational transport

protein transported while it is still being made

signal receptor protein

grabs ER protein and pulls protein along with ribosome to touch ER

SRP receptor

where SRP and protein click into initially at ER

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loads protein into translocon

translocon

channel in the ER membrane that proteins are backed into

BiP

helps pull protein through translocon

start transfer sequence

hydrophobic sequence that says “put the amino acids after me in the ER lumen”

* can be cleaved if on N terminus

positive

charge of cytosol

negative

charge of ER lumen

stop transfer sequence

hydrophobic sequence that says “**don’t** put amino acids after me in the ER lumen”

multipass transmembrane protein

crosses the membrane multiple times

protein glycosylation

process of adding sugars to ER protein


1. Asn enters lumen through translocon
2. oligosacharotransferase adds on a 3 sugars (glucose, mannose, N-acetylglucosamine) from dolichol
3. translocation finishes

dolichol

lipid that lives in ER membrane that holds sugars to be put on proteins

making sugars for protein

1. on cytosolic side add P group to dolichol using CTP
2. add P group and 2 glucosamine using UDP
3. add 5 mannose using GDP-Mannose
4. flip to ER lumen
5. add 4 mannose using GDP-Mannose
6. add 3 glucose using UDP-glucose

calnexin

holds protein by single glucose while other proteins check if the folding is correct

* cleaves glucose after done

glucosidase

trims two sugars off the labeled “new protein” before loading into calnexin

glucose transferase

adds a single glucose onto proteins after incorrectly folded using UDP-glucose

* can be checked on calnexin again

ubiquitin

flags misfiled proteins for proteasome

proteasome

breaks bad proteins back into amino acids if tagged with ubiquitin

removal of bad proteins

1. checked on calnexin
2. ubiquitin attached
3. pushed out through translocon
4. proteasome eats

protein formation in ER

1. SRP grabs and translation paused
2. loaded onto SRP receptor
3. protein moved to translocator
4. translation finishes


1. protein inserted into ER based on start and stop sequences if transmembrane
2. phosphate group, N-acetyl glucosamine, mannose, and glucose attached at Asn
5. ribosome detaches
6. start sequence possibly cleaved
7. (2) glucose trimming
8. protein loaded onto calnexin for final checks

COP II

protein that helps pinch vesicles from the ER by coating the membrane

cargo receptor

hold onto proteins that will be inside the vesicle lumen

KDEL

signal for ER lumen protein retrieval

KKXX

signal for ER membrane protein retrieval

vesicle transport from ER to Golgi

1. COPII proteins including SarGTP attach to ER membrane
2. pinch
3. proteins sucked in and attached to receptors
4. pinch continues
5. SarGTP removes COPII protein coat and becomes GDP


1. vesicle closes
6. vesicle walked to Golgi

vesicle transport from Golgi to ER

1. COPI attaches to Golgi membrane
2. pinch part way
3. proteins attach to receptors for KDEL or KKXX
4. pinch
5. COPI falls off


1. vesicle closes

adaptor protein

help grab proteins into forming vesicle from ER to Golgi and back

clatharin

coats vesicles for secretion and endosome

adaptin

sits between clatharin coat and receptors in vesicle

kinesin

walks proteins headed towards membrane

ie ER>golgi>membrane

SNAREs

labels vesicles and prevents them from fusing with each other

dynen

walks vesicles inwards

ie membrane>…

motor proteins

walk vesicles along microfilaments while using ATP

phosphorylation

labels lysosome with P group

sulfation

can help strengthen future binding

Golgi apparatus

main functions

* phosphorylation- like for lysosome proteins
* remove mannoses
* glycosylation
* sulfation

cis Golgi

“beginning” of Golgi stacks

trans Golgi

“end” of Golgi stacks

complex oligosaccharide

sugar complex added to protein in Golgi with lots of other types of sugars

high mannose oligosaccharide

sugar complex added to protein in Golgi with lots of mannoses

lysosome

degrades organelles and material brought in vesicles

* acidic environment bc of protein pump

phogocytosis

taking in large substrate from outside cell

pinocytosis

taking in small substation from outside cell

early endosome

vesicles with outside material still near plasma membrane

protease

does protein degradation

nuclease

does nucleus acid degradation

lipase

does lipid degradation

mannose-6-phosphate

lysosome localization signal

* phosphates most important

lysosomal hydrolase

signal patch and N-linked oligosaccharide + mannose

GlcNAc phosphototransferase

attaches UDP-GLcNAc to signal patch

making M6P

1. N-linked oligosaccharide + mannose residue attach to phosphototransferase
2. UDP-GLcNAc loads onto phosphototransferase
3. bind GlCNAc-P and release UMP
4. release lysosome hydrolase with GLcNAc-P
5. remove GlcNAc
6. M6P left on signal patch

lysosome protein delivery

1. M6P attached to protein from ER
2. protein binds to M6P receptor
3. clatharin coats aided by adaptin


1. vesicle begins to form
4. clathrin coat releases


1. vesicle closes
5. vesicle walked to lysosome via kinesin
6. vesicle meshes to early lysosome
7. protein dissociates from receptor


1. high pH
8. P group removed to put…. in inactive state

endosome

organelle that becomes lysosome when more proteins are added

retromer

coats vesicle that will take M6P receptor back to Golgi

O-linked glycosylation

adding sugars to new amino acid on protein

N-linked glycosylation

adding sugars to Asn where sugars were added in ER

glycosidase I

trims first glucose off of protein tagged in ER

glycosidase II

trims second glucose off of protein tagged in ER

signal peptidase

cleaves signal off of protein in destination

nucleus

double membrane organelle with large pores

rough ER

single membrane bound with SRP receptors

Golgi apparatus

single membrane bounds with many stacks (cis and trans regions)

lysosome

single membrane bound organelles that comes from endosome and peroxisomes

mitochondria

double bound organelle with oxidative phosphorylation

chloroplast

double membrane bound organelle in plants

Rab protein

name tag for vesicles going to plasma membrane and anchor point

v-SNARE

protein that sticks off of vesicle to help bind to plasma membrane

tether protein

anchors onto Rab and pulls vesicle to plasma membrane

t-SNARE

extends from plasma membrane to attach to v-SNARE and pull vesicle in

unfolded protein response

ER grows and takes up more supplies when there are lots of proteins/mistakes being stored there

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may lead to apoptosis

constitutive exocytosis

constant release from Golgi to extracellular via vesicle