BIOL 4100 EXAM 5 QUESTIONS AND ANSWERS WITH
COMPLETE SOLUTIONS VERIFIED
what goes into the cellular garbage systems?
misfolded, unused, turnover proteins; metabolic products; organelles
describe the cellular garbage system
substrate enters cells through endocytosis; either ubiquitin added from free pool and
goes through proteasome with epoximicin/lactacystin to break up substrate OR ubiquitin
is added to mitochondria and exposed to Wortmannin/bafilomyocin to go through
autophagy OR endocytosized substrate exposed to wortmannin/bafilomycin which
becomes lysosome
consequences of impaired protein degradation
protein aggregates (group up--body can't get rid of easily), ubiquitinated inclusions,
vacuolation (paraptosis--cell death process/formation of vacuoles), damaged
organelles, impairment of cellular processes, cell death
impaired protein degradation is the _____ ________ of degenerative diseases
such as neurodegeneration, muscle and liver degeneration, lung disease and
aging
underlying pathogenesis
-turnover of individual protein is/is not constant. what is an ex of this?
-half lives of proteins can vary from _____ to _____
-what is normal protein half life?
is not (proteins we need aren't degraded), minutes to infinity, 100-200 minutes
,how are short and long lived proteins different?
short=regulatory proteins, enzymes that catalyze committed steps in cellular processes,
transcription factors (turn on/off quickly); long=structural proteins (actin), nuclear pore
proteins, histones (
protein degradation may depend on _____ _______.
is a _____ process.
works with ______ or _____ proteins
tissue distribution, regulated, faulty/damaged
most protein degradation--80-90%--happens through _____/_____ pathway. 10-
20% happens through ____/_______ pathway.
ubiquitin/proteasome, endosomal/lysosomal
name the protein degradation pathway
-80-90% of protein degradation
-most intracellular proteins
-mostly protein driven
-excess/misfolded proteins
ubiquitin/proteasome pathway
name the protein degradation pathway
-10-20% of protein degradation
-extracellular proteins (endocytosis)
-cellular organelles/larger groups of molecules
-"some" intracellular proteins
endosomal/lysosomal pathway
,how are individual proteins selected for degradation?
chosen because they get modified by addition of ubiquitin to 3' structure
ubiquitin is a ________ _______ 76 amino acid polypeptide with a molecular
weight of 8.5 kD
-it is conserved across all species of _____ (96%)
-structurally characterized by presence of what?
highly conserved, eukaryotes, one alpha helix, 5 beta sheets and 4 aa carboxyl tail
domain (LRGG--leucine, arginine, glycine, glycine) with Glycine 76 very last
what are the 7 lysine residues in ubiquitin? where do they reside?
Lys63, 48, 29, 27, 6, 11, and 33; on outside of structure
what is monoubiquitination (or multi mono) involved in?
K48, K11, maybe K27/29 polyubiquitination involved in?
K63 polyubiquitination?
transcription, endocytosis, trafficking (some type of cell regulation); proteasomal
targeting; signaling (NFkB activation), DNA repair, endocytosis (lysosomal targeting)
when talking about ubiquitin modification, we assume _____ linkage? ubiquitin is
always added to lysine residues using _______. how is the shape of the ubiquitin
chain decided?
homologous, G76, which lysine group is built off of
do different shaped ubiquitin chains have different functions?
yes
what are the 3 parts of the ubiquitin pathway and what is it called?
, E1 ubiquitin activating enzyme, E2 ubiquitin conjugating enzyme, E3 ubiquitin protein
ligase
describe the general steps of ubiquitin pathway
E1+Ub+ATP yields E1/Ub+ AMP+Pi add E2; yields E1 and E2 bound to Ub; binds to E3
with bound substrate; ubiquitin binds to substrate on E3; substrate released from E3
and further ubiquitination
ubiquitin activating enzyme 1:
1. E1 activates the C-terminus of ubiquitin by forming an ____ _____ intermediate
2. catalytic ______ residue "attacks" the ubiquitin causing release of AMP and
formation of what?
3. reaction is ____ as another ubiquitin is adenylated and the charged ubiquitin is
transferred to an ___ forming another thioester bond
-extremely _______ enzyme--turnover rate is 1-2/second
acyl-adenylate, cysteine, formation of an E1 ubiquitin thioester intermediate, repeated,
E2, efficient
why does the E1 reaction have to be very efficient?is this reaction ATP
dependent? why?
because there aren't many E1s, yes, loosing double Pi with energy required to add Ub
ubiquitin conjugation enzyme E2:
1. carries activated ubiquitin for the E1 to the ____
2. each _____ ____ has a Cys residuce located in a shallow groove at its active
site which will form a thioester bond with the ubiquiting molecule being _______
COMPLETE SOLUTIONS VERIFIED
what goes into the cellular garbage systems?
misfolded, unused, turnover proteins; metabolic products; organelles
describe the cellular garbage system
substrate enters cells through endocytosis; either ubiquitin added from free pool and
goes through proteasome with epoximicin/lactacystin to break up substrate OR ubiquitin
is added to mitochondria and exposed to Wortmannin/bafilomyocin to go through
autophagy OR endocytosized substrate exposed to wortmannin/bafilomycin which
becomes lysosome
consequences of impaired protein degradation
protein aggregates (group up--body can't get rid of easily), ubiquitinated inclusions,
vacuolation (paraptosis--cell death process/formation of vacuoles), damaged
organelles, impairment of cellular processes, cell death
impaired protein degradation is the _____ ________ of degenerative diseases
such as neurodegeneration, muscle and liver degeneration, lung disease and
aging
underlying pathogenesis
-turnover of individual protein is/is not constant. what is an ex of this?
-half lives of proteins can vary from _____ to _____
-what is normal protein half life?
is not (proteins we need aren't degraded), minutes to infinity, 100-200 minutes
,how are short and long lived proteins different?
short=regulatory proteins, enzymes that catalyze committed steps in cellular processes,
transcription factors (turn on/off quickly); long=structural proteins (actin), nuclear pore
proteins, histones (
protein degradation may depend on _____ _______.
is a _____ process.
works with ______ or _____ proteins
tissue distribution, regulated, faulty/damaged
most protein degradation--80-90%--happens through _____/_____ pathway. 10-
20% happens through ____/_______ pathway.
ubiquitin/proteasome, endosomal/lysosomal
name the protein degradation pathway
-80-90% of protein degradation
-most intracellular proteins
-mostly protein driven
-excess/misfolded proteins
ubiquitin/proteasome pathway
name the protein degradation pathway
-10-20% of protein degradation
-extracellular proteins (endocytosis)
-cellular organelles/larger groups of molecules
-"some" intracellular proteins
endosomal/lysosomal pathway
,how are individual proteins selected for degradation?
chosen because they get modified by addition of ubiquitin to 3' structure
ubiquitin is a ________ _______ 76 amino acid polypeptide with a molecular
weight of 8.5 kD
-it is conserved across all species of _____ (96%)
-structurally characterized by presence of what?
highly conserved, eukaryotes, one alpha helix, 5 beta sheets and 4 aa carboxyl tail
domain (LRGG--leucine, arginine, glycine, glycine) with Glycine 76 very last
what are the 7 lysine residues in ubiquitin? where do they reside?
Lys63, 48, 29, 27, 6, 11, and 33; on outside of structure
what is monoubiquitination (or multi mono) involved in?
K48, K11, maybe K27/29 polyubiquitination involved in?
K63 polyubiquitination?
transcription, endocytosis, trafficking (some type of cell regulation); proteasomal
targeting; signaling (NFkB activation), DNA repair, endocytosis (lysosomal targeting)
when talking about ubiquitin modification, we assume _____ linkage? ubiquitin is
always added to lysine residues using _______. how is the shape of the ubiquitin
chain decided?
homologous, G76, which lysine group is built off of
do different shaped ubiquitin chains have different functions?
yes
what are the 3 parts of the ubiquitin pathway and what is it called?
, E1 ubiquitin activating enzyme, E2 ubiquitin conjugating enzyme, E3 ubiquitin protein
ligase
describe the general steps of ubiquitin pathway
E1+Ub+ATP yields E1/Ub+ AMP+Pi add E2; yields E1 and E2 bound to Ub; binds to E3
with bound substrate; ubiquitin binds to substrate on E3; substrate released from E3
and further ubiquitination
ubiquitin activating enzyme 1:
1. E1 activates the C-terminus of ubiquitin by forming an ____ _____ intermediate
2. catalytic ______ residue "attacks" the ubiquitin causing release of AMP and
formation of what?
3. reaction is ____ as another ubiquitin is adenylated and the charged ubiquitin is
transferred to an ___ forming another thioester bond
-extremely _______ enzyme--turnover rate is 1-2/second
acyl-adenylate, cysteine, formation of an E1 ubiquitin thioester intermediate, repeated,
E2, efficient
why does the E1 reaction have to be very efficient?is this reaction ATP
dependent? why?
because there aren't many E1s, yes, loosing double Pi with energy required to add Ub
ubiquitin conjugation enzyme E2:
1. carries activated ubiquitin for the E1 to the ____
2. each _____ ____ has a Cys residuce located in a shallow groove at its active
site which will form a thioester bond with the ubiquiting molecule being _______
