Lecture 7 Flashcards
True or False: Translation is usually the last step for producing a functional molecule.
False
What structures of a protein are modified after it has been assembled?
Primary, Secondary, and Tertiary
What does a healthy cell do to dysfunctional proteins?
It damages and degrades proteins that are not functional
What are primary protein chains composed of?
Amino acids
What structures can chains of amino acids fold into?
secondary (alpha helix or beta sheet) and tertiary structures
What do folded tertiary structures assemble into?
Quaternary structures
What happens when the N-formyl group is removed by
methionine deformylase?
can escape
immunorecognition
What occurs with the addition of phosphoryl or
methyl groups?
can change the
activity of signal transduction
What two substances can regulate protein activity?
Adenylylation and acetylation
What can be attached to proteins?
Lipids and sugars
What is mass spectrometry used for?
-identify proteins in cell
extracts (proteomics)
-identify posttranslational
modifications
Who showed that folding can be governed
by the protein itself?
Christian Anfinsen
True or False: Majority of the proteins self assemble
True
True or False: Proteins can be misfolded
True
What molecules help
misfolded proteins to re-fold properly?
Chaperones
What are chaperones also referred to as?
Heat-shock proteins (HSP)
Characteristics of heat shock proteins (HSPs) include:
- Levels increase with temperature
increase - More heat-resistant compared to
average protein
In E. coli chaperones, how many families are involved in protein refolding?
3
What is Trigger factor (TF)?
A family of protein chaperones that are ribosome associated, promote folding, and prevent aggregation
What is GroEL and GroES?
A family of protein chaperones that have the following characteristics:
▪ Form stacked ring with a hollow center
▪ The protein fits inside the pore
▪ Cycles of ATP-hydrolysis cause
conformational changes to the barrel that
reconfigure the target protein
What is DnaK and DnaJ?
A family of protein chaperones that clamp down on a polypeptide to assist folding
True or False: Misfolded proteins are targeted for degradation
True
What processes misfolded proteins?
barrel-shaped Clp proteases (sense exposed by hydrophobic regions)
True or False: Folded proteins have different half-life
True
What amino acids have a short half life?
Leu, Phe, Trp, Tyr
What amino acids have a long half life?
Asp, Glu, Cys
What is protein stability is correlated with?
the presence of a degron, or N-terminal aa
remaining after fMet cleavage
True or False: Clp proteases are conserved by most organisms.
True
How are Clp proteases classified?
on the active site
residues
What are the three Clp proteases?
1.Serine proteases
2.Cysteine proteases
3.Threonine proteases
How are Clp proteases assembled?
ATPase cap proteins
(e.g. ClpA or ClpX)
What are Proteasomes?
protease complexes
that degrade proteins
What is the first step of the Folding vs Degradation Triage Pathway?
DnaK and DnaJ chaperones bind to nascent protein
What is the second step of the Folding vs Degradation Triage Pathway?
Proteins may be folded into an active form
What is the third step of the Folding vs Degradation Triage Pathway?
If not folded properly, the protein can be fed to GroEL for remodeling
What is the fourth step of the Folding vs Degradation Triage Pathway?
If still not properly folded, the protein may be passed through proteases through degradation
True or False: Bacteria secrete proteins to influence their environment
True
Secreted proteins are proteins that are translocated across the inner membrane
and end up in:
- periplasm
- cross-linked to the cell wall
- anchored in the outer membrane
- released into the milieu/environment
Secreted proteins usually contain:
a signal peptide at the N-terminus that targets
these proteins to be translocated across the inner membrane
What can target proteins destined for the cell-wall
or outer membrane?
amino acid sequence motifs
What is present for Sec-dependent
translocation across membrane?
signal peptides
What charge is the n-region?
positive
Is the h-region hydrophilic or hydrophobic?
hydrophobic
What processes the c-region?
signal
peptidase (SPase)
What are some other amino acid motifs?
*Sorting signal for cell-wall
anchoring
* LipoBox for anchoring in the
membrane
What are the two major secretion pathways in bacteria?
- General Secretion (Sec)
pathway
*Twin Arginine Translocase (TAT)
pathway
What does the General Secretion (Sec) pathway secrete?
unfolded proteins
What does the Twin Arginine Translocase (TAT) pathway secrete into the periplasm?
folded proteins
True or False: Both, membrane proteins and
secreted proteins employ Sec
pathway
True
What do proteins destined to be
incorporated into the inner
membrane employ?
cotranslational Sec pathway
Hydrophobic transmembrane
domains can incorporate into the
membrane bilayer through what channel?
SecYEG
lateral channel
What do proteins destined to be secreted into the
periplasm employ?
general SecA-dependent
pathway
What components are involved in the general SecA-dependent
pathway?
*SecB pilot protein (chaperone)
* SecA (has ATPase activity)
* SecYEG translocon
Where is the peptide is completely translated?
Cytoplasm (post-translational export)
The completed pre-protein is then captured by what?
piloting protein called SecB
SecB unfolds and delivers the protein to _______ (w/ ATP) , which is associated with the _______________.
SecA, SecYEG translocon
What cleaves off the signal peptide to
release a mature protein?
Signal peptidase
True or False: A proton motive force (PMF) is used to move the signal sequence of the folded protein through the TatA translocase and into the periplasm
True
What happens to some proteins in gram negative bacteria that end up farther than the periplasm?
- Incorporate into the outer membrane
(E.g. outer membrane proteins (OMPs) - Exported out of the cell completely
(E.g. nutrient acquisition proteins, toxins)
True or False: Different bacteria have evolved different secretion mechanisms beyond the periplasm.
True
What type of proteins usually form beta-barrel
structures?
outer membrane proteins (OMPs)
What stops OMP aggregation in the
periplasm?
Chaperones
What function does the Beta Barrel Machine (BAM) serve?
facilitates assembly of
OMPs in the outer membrane
What are Type I secretion systems in gram negative bacteria?
ABC type transporters and
are the simplest of known
secretion systems
What are characteristics of ATP-Binding Cassette (ABC)
transporters?
- Outer membrane channel
- Periplasmic protein
- ATP-binding protein at the
inner membrane
What type of gram positive bacteria utilize the type 7 secretion system?
Actinobacteria and Firmicutes
T7SS translocon:
- Inner membrane
- at least 4 subunits
- Conserved ATPase EssC
A subset of specialized proteins that lack Sec-dependent signal peptides that is secreted in the type 7 system?
WXG and LXG
What roles does the type 7 secretion system serve in bacteria?
pathogenesis and
competition between bacteria
