I am a Master's student in Biochemistry at the Karolinska Institutet in Stockholm, Sweden. I have a range of notes from courses that I undertook as part of my Bachelor's studies. These notes are detailed and in depth that focus on many aspects of how proteins are ubiquitinated and broken down. Thes...
Test Bank - Lehninger Principles of Biochemistry, 8th Edition (Nelson, 2022), Chapter 1-28 | All Chapters
TEST BANK FOR LEHNINGER PRINCIPLES OF BIOCHEMISTRY NELSON 6TH EDITION
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Ubiquitin Proteasomal system for protein degredation:
Structure of the proteasome:
The two outer rings are composed by seven α-subunits
(named α1 to α7), while the two inner rings are
composed by seven β-subunits (β1-β7)12. β-rings
contain the proteolytic active sites: β1, β2 and β5
present caspase-like, trypsin-like and chymotrypsin-
like activities, respectively. The β1 sites cleave after
acidic residues (Glu, Asp) and are referred to as
“postacidic,” PGPH (“post-glutamate peptide
hydrolase”), or “caspase-like” (Casp-L). see notes
from BC4016 on amino acid digestion for significance
of tryp + chymotryp activity! The 20S proteasome core
complex encloses a cavity consisting of 3
compartments joined by narrow passageways.
Although 20S particles can exist in a free form, its
default status is closed and requires the binding of
proteasome activators to degrade polyubiquitylated
proteins. Therefore, 20S particles are considered to be
inactive, unable to degrade polyubiquitylated proteins.
In crystal structures of the proteasome core complex
alone, there is no apparent opening to the outside. The
ends of the cylindrical complex are blocked by N-
terminal domains of a subunits that function as a gate.
Interaction with a cap complex causes a conformational
change that opens a passageway into the core complex.
The 19S regulatory cap complex recognizes multi-ubiquitinated proteins, unfolds them, removes ubiquitin chains, and provides a
passageway for threading unfolded proteins into the proteasome core complex. The 19S cap is a 20-subunit 700 kDa complex,
also referred to as PA700.
The outermost "lid" of the 19S cap consists of a ring of eight proteins.
The innermost "base" of the 19S cap includes a ring of six members of the AAA family of ATPases. These
are chaperones that carry out ATP-dependent unfolding of proteins prior to their being threaded into the core complex. It
is typical of AAA ATPases that they assemble into hexameric rings.
Isopeptidases in the 19S cap disassemble ubiquitin chains. Ubiquitins can then be re-used. At least one deubiquitylating
enzyme is known to be located between the lid and base regions of the 19S cap.
A simpler archaebacterial cap complex called PAN consists only of a hexameric ring of AAA ATPases, comparable to the base
of the 19S regulatory cap. PAN, in the presence of ATP, was found to cause opening of a gate at the end of the 20S proteasome
through which an unfolded protein could enter. The base of the19S cap is assumed to do the same, although high resolution
structural evidence for this is still lacking.
The 11S regulatory cap is a heptameric complex of a protein PA28. It allows small, non-ubiquitinated proteins and peptides to
pass into the proteasome core complex. This does not require ATP hydrolysis.
The 11S cap is dome-shaped, with a wide opening at each end. Binding of the 11S cap alters the conformation of N-terminal
domains of core complex a subunits, opening a gate into the proteasome core. Formation of mixed complexes, in which a
proteasome core is sandwiched between 19S and 11S caps, has been demonstrated by electron microscopy. In vivo, a 19S cap may
recognize, de-ubiquitinate, unfold and feed proteins into a core complex at one end, while an 11S cap at the other end may provide
an exit path for peptide products.
Active proteasomes are formed by the interaction of proteasomal regulatory particles with a core particle (20S), which
contains the proteolytic active sites. Free intracellular 20S are normally found in an inactive/closed state and require the
binding of 20S activators to degrade proteins. The major assembly of the 20S proteasome is with the 19S regulatory protein,
which recognizes the polyubiquitylated substrate, removes the ubiquitin moieties and unfolds the substrate to translocate it
into the 20S proteolytic chamber. The 20S can also be activated by the PA28 complex or the Blm10/PA200 protein. Finally,
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