Protein Life Structure Flashcards
Where does protein folding start?
- Proteins begin to fold while they are being synthesized on the ribosome
- As portions of newly synthesized proteins are emerging from ribosome, many AA residues involved in secondary and tertiary structure become available to interact w/ ea other
Molten Globule
- initial form that many globular proteins attain ad they begin to fold
(This is not its final folded state and proteins in this meta-state are unlikely to be active)
Molecular Chaperones
- Transition from molten globule —> final folded protein is not efficient and requires aids
- members of heat shock family of proteins that participate in protein folding reactions and reduce/prevent protein aggregation
- named by weight
- actions require ATP
Proteasome-Dependent Protein Degradation Pathway
- 19S cap serves as entry site and unfolds proteins via ATP hydrolysis
- then sent to 20S core for proteolysis
Proteasome
- large multi-sub unit abundant machine that degrades targeted proteins in an ATP-dependent manner (IN CYTOPLASM)
- 20 S core is segment where proteolysis occurs
- 19 S cap is regulatory center of proteasome
Ubiquitin
- 76 AA protein that is covalently attached to specific lysine residues on target proteins through its carboxyl terminus
- Need a polyubiquitan chain (min chain length of 4 ubiquitin) on targeted proteins
E1
Ubiquitin-Activating Enzyme
- uses ATP hydrolysis to “activate ubiquitin” by creating a covalent attachment of ubiquitin to specific -SH group on E1
- Least common
E2
Ubiquitin-Conjugating Enzyme
-interacts w/ E1 leading to the transfer of ubiquitin to a specific -SH group on E2
More rare than E3
E3
-Ubiquitin Ligase
- Ubiquitin-charged E2 forms a complex w/ an E3
(In some cases the ubiquitin is transferred from E2 to E3)
-Most abundant
Final Steps of Ubiquitin Path
- 1- Distinct E3 recognizes the “degradation signal” on target protein
- “Degradation signal”- specific stretch of AA
- Target protein is now bound to E2/E3 complex
- 2- Ubiquitin is transferred from E2 (or E3) —> specific lysine residue on target protein forming a covalent bond
- 3- Process is repeated as additional ubiquitin molecules are linked to specific lysine residues on protein-linked ubiquitin via a covalent bond
- Result= targeted protein contains covalently-attached multi-ubiquitin chain
SRP
- multi-subunit RNA protein particle; soluble cytoplasmic protein
- recognizes signal sequence of growing polypeptide as it emerges from ribosome —> arrest in protein translation (PAUSE)
- SRP-bound to the signal sequence and ribosome then interacts w/ SRP receptor on outer membrane of ER —> transfer of translating protein to translocation machinery
BiP
- chaperone protein that binds unfolded segments of polypeptide as they emerge into ER lumen
- ATP driven cycles of binding and releasing BiP acts to pull translocating protein into ER lumen
Co-translation Transport Into ER
-Import of proteins to rough ER occurs B/F synthesis is complete (co-translation transport)
1- signal sequence (hydrophobic) on polypeptide chain is recognized by SRP as it leaves ribosome
2-SRP-signal sequence interact w/ SRP receptor on outer ER membrane
3- translating protein moved to translation machinery
4-Once ribosome docks on translocation channel protein … translation resumes and translocation into ER begins as translocation channel opens
“start” and “stop” transfer sequences
Hydrophobic and responsible for transmembrane insertion of
- Start transfer sequence- ER signal sequences that interact w/ translocation machinery itself by opening translocation channel and beginning transport into ER
- Stop transfer sequence- hydrophobic; on translocating proteins; recognized by specific components of translocation machinery
Where are start and stop transfer sequences found?
-Both are found on the translated protein itself
Protein Glycosylation
- covalent attachment of sugar molecules
- occurs in ER and extended in Golgi
- 1st sugars to be attached to ER proteins are added as precursor oligosaccharide containing 14 sugars
1-sugar made in cytoplasm but transferred and held in ER membrane (luminal side) by lipid dolichol
2-N-linked glycosylation- precursor oligosaccharide is covalently attached to specific Asn residue on emerging translocating protein
2 major classes of N-linked oligosaccharides
1- high mannose
2-complex oligosaccharides
**distinguished by sensitivity v resistance to cleavage by specific endoglycosidase
Cop I v Cop II Coated Vesicle
- Cop I coated vesicles bud from Golgi (Arf responsible for assembly of COPI coated vesicles)
- *GTP hydrolysis triggers Sar-1 release from membrane and coat disassembly
-Cop II coated vesicles bud from ER (Sar-1 responsible for COPII coated vesicles)
Rab proteins
-monomeric G proteins
1-interact w/ donor membrane
2- insert on target membrane
3- docking initiated GTP hydrolysis which releases Rab
-aids in initial docking of vesicle
SNARE proteins
v-snares on vesicles and t-snares on target membranes
- v-SNARE and t-SNARE complexes combine to form helical bundles that aid in membrane docking and fusion
- SNARE complexes are dissembled after membrane fusion using the energy of ATP hydrolysis from NSF protein and other accessory proteins
ERAD Path
ER-associated degradation
misfiled proteins exported from ER —> cytoplasm through translocation machine and targeted for degradation by proteasome
1-recognized by recognition components in ER lumen
2- targeted to translocation machinery –> transported to cytoplasm
3- tagged w/ ubiquitin in cytoplasm and subsequently degraded by proteosome
Calnexin and calreticulin
- 2 Ca++ binding proteins that bind to incompletely folded proteins in ER lumen that contain single glucose residue
- Cleavage of terminal glucose required to release calnexin and calreticulin which then triggers glycoprotein exit from ER
UPR
Unfolded Protein Response
generated when ER accumulates high levels of unfolded proteins
Hemoglobin S
- deoxygenated mutant form of hemoglobin
- caused by homozygous recessive mutation in beta-globulin gene (changing glutamate at position 6 —> valine missense mutation
- prone to aggregate and forms fibrous precipitates
- Accumulation of fibrous HbS —> RBCs lose elasticity and form “sickle” shape that occludes capillaries
CFTR
Cystic Fibrosis Transmembrane Conductance Regulator
- can have 5 possible mutation
- Mutations affect expression, intracellular trafficking and functioning of CFTR protein
- most common mutant is F508 CFTR protein forms aggregates w/in ER and is subsequently degraded
Cross Beta Filament
- Formed when a series of polypeptide chains are layered over one another as cont stack of beta-sheets (ex- in an amyloid plaque)
- Example of how non-mutant proteins can form aggregates and contribute to disease pathology
Huntingtin
- http
- expansion of CAG repeat in the huntingtin gene (http) —> production of mutant protein w/ expanded poly-glutamine (polyQ) repeat
- PolyQ-expanded http form intracellular aggregates that disrupt many cellular processes in vulnerable neurons
Prion Protein
-structural change in normal prion protein (PrP) triggers aggregation of aggregate-prime “abnormal” prion protein (PrP*)
Beta-amyloid Plaque and AD
- Dominant protein component of extracellular amyloid plaque is the 40-43 AA on alpha-beta peptide
- The alpha-beta peptide is derived from proteolytic cleavage of the transmembrane Amyloid Precursor Protein (APP)
**Most AD sporadic and not caused by mutation
In what direction do proteins move w/in Golgi?
-Enter cis Golgi and cont to trans Golgi where they are packaged and sent to target
