Section 4: How do eukaryotic cells organize comparments?

Cytosol

___ site for many metabolic pathways, protein synthesis and the cytoskeleton reside here

Nucleus

___ holder of main genome; DNA and RNA synthesis

Endoplasmic Reticulum (ER)

___ synthesis of proteins and most lipids

Golgi apparatus

___ modifies, sorts and packages proteins and lipids received from ER for secretion or delivery to other organelles

Lysosomes

___ responsible for intracellular degradation of old cellular material (recycles)

Endosomes

___ sorting of material internalized into the cell

mitochondria

ATP synthesis through oxidative phosphorylation

chloroplast

ATP synthesis and carbon fixation through photosynthesis

peroxisomes

oxidative breakdown of toxic molecules; breaks down lipids and toxic materials and produces hydrogen peroxide

rRNA

___ made in the nucleous

nuclear pore

consists of over 1000 proteins and allow for free passage on molecules smaller that 40 kDa

nuclear localization signal

sorting signal that newly made proteins need before entry into the nucleus

nuclear lamina

a protein that connects chromatins and nuclear membranes

Rough ER

___ ribosomes on its surface and connected to the nuclear envelope

• The proteins made from ribosomes attached to the ER are secretory and membrane-bound proteins

• The proteins made from free ribosomes stay in the cytosol

Smooth ER

___ no ribosomes on their surface; most likely the site of lipid (steroid hormone) synthesis

sorting signals

___ are a stretch of amino acids on protein that directs them to a particular destination in the cell

• Proteins without a ___ and stay in the cytosol forever

cytosolic proteins

organelles like nucleus, chloroplast, mitochondria, and peroxisomes are places ___, can pass through

lumenal proteins

organelles like golgi apparatus, and ER are places ___, can pass through

Nuclear import receptors

___ (also called importin) are cytosolic proteins that recognize the nuclear localization signal on protein and guide them to the nuclear pore:

Ran

is a hydrolyzing enzyme that either binds to GTP and releases GDP

signal recognition particle

binds a ribosome to SRP receptor on the ER surface

o Signal sequence opens the protein translocation channel into the ER membrane

signal peptidase

removes the signal sequence once on the ER lumenal side (inside the ER)

stop transfer sequence

can exist on the polypeptide, that stops the transfer of the protein

o This closes the pore, and leaves the protein embedded in the membrane

internal sequence system

an ___ is where translocation starts which leads to multiple parts of the polypeptide to be left embedded in the membrane

hydrophobicity plot

___ is an analysis that says how much hydrophobicity is present on certain amino acid sequences on the polypeptide

o Helps us know how the protein will face (Topo 1 or 2)

o Red and yellow- predicts hydrophobic groups

o Green indicates hydrophilic group

o Charge separation of the first α-helix is needed to determine the topology of the whole polypeptide

Positive N-terminal

___ side makes a signal peptide; faces outside the ER lumen

 Leads to the opening of the ER translocon; sewing machine mechanism

Negative N-terminal

___ side makes a transmembrane helix; faces inside the ER lumen

 No pore opening

BiP

___ is the most abundant chaperone proteins in the ER lumen

Heat shock chaperone proteins

help the proteins survive in suboptimal temperatures and to not denature

oxidizing space

o   Just like the extracellular environment, the ER lumen is an ___ which means it is able of permitting disulfide bonding formation

This stabilizes protein folding and misfolding

Protein disulfide isomerase (PDI)

___ continuously breaks disulfide bonds to find the correct conformation; like a chaperone

N-glycosylation

___ is a complex set of sugars attached to the Asn of the tripeptide: Asparagine-(any amino acid)-Serine/Threonine

o Exists inside the ER lumen

o Happens once the protein is added into the ER lumen

must be trimmed before peptide can exit the ER

nitrogen bond

Called N-glycosylation because the oligosaccharide is attached to the polypeptide through a ___ with the amino acid (Asn), not because it occurs at the N-terminal end of the polypeptide

oligosaccharyl transferase (OST) complex

performs N-glycosylation though bulk transfer at the same time as peptide enters through the ER translocon

ER retention signal

signal present at the C-terminus of an ER-residing chaperone

o -Lys-Asp-Glu-Leu-COO-

IRE1

part of the unfolded protein response; a transmembrane cytosolic protein kinase that initiates the process that cuts off exons of mRNA transcription initiation factors and allows them to be translated into transcription initiation factors

PERK

part of the unfolded protein response; a transmembrane protein that inactivates a translation initaion factor

ubiquitin tag

ubiquitin proteasome system degrades proteins (in proteosome) based on whether or not they have a ___

ERAD

recylces membrane proteins and eliminates misfolded protein in the E; composed of protein channels, ubiquitin, and a pulling force

MAD

proteosome for mitochondria-associated degredation with TOM

CHLORAD

Proteosome for chloroplast-associated degredation via TOM and Ub-ligase

vesicle transport

transport that happens through budding and fusion

trans golgi network

uncoated vesicles are found at the ___, and are responsible for default, bulk secretion

clarthrin-coasted vesicle

caged molecule that transports molecules into the plasma membrane

cargo receptor protein

part of clathrin-coated vesicle that holds the cargo

adaptin

part of clathrin-coated vesicle that mediates the binding of cargo receptors to the clathrin coat

dynamins

motor proteins in clathrin-coated vesicle that cleaves the membrane and pinches off the vesicle being formed; requires energy from GTP

COP II coated vesicle

transports proteins from ER to cis golgi apparatus

COP I coated vesicle

transports protein from golgi apparatus back to ER

KDEL receptor

most popular COP I coatomer; returns BiP back to the ER if it was accidentally transported to the golgi

mannose 6-phosphate

we know a protein is going to a lysosome after the golgi if it has been tagged with ___

phagocytosis

engulfs large particles into a phagosome which is a lysosome that allows for degradation of the particle

pinocytosis

engulfs smaller peptides and sugars without specific transporters; degrades the molecules

o Through formation of clathrin-coated pits

o A constant process

o Takes things to lysosome

receptor-mediated endocytosis

engulfs specific ligands and receptors into endosomes which redistributes them across the cell

o Through induced formation of clathrin-coated vesicles

o This is how cholesterol in taken into the cell

Rab-GTPase

___ is a family of lipid-anchored membrane proteins that each specify a route for a protein to take

o The lipid-based membrane association allows for flexible targeting to distinct destinations; allows the protein to go to any membrane and not just remain in the cytosol

Rab

___ on the vesicle is recognized by tethering protein on the target membrane

docking

energetically unfavourable step of vesicle transfer that requires ATP hydrolysis, and the use of SNARE proteins that help the membranes fuse