Exam 1 Lectures 6 Flashcards
the Chou-Fasman method predicts
2ndary structures in proteins
Frequency (f) =
part/whole thus (aa in alpha-helix)/(all aa)
Propensity (P)=
(propensity)/(natural inclination)
spatial arrangement of aa residues that are far apart in the sequence and to the pattern of disulfide (S-S) bonds describes
tertiary structure
why is 3’ more compact than 2’
3’ is tightly packed and folded vs 2’ which has alpha helices and beta sheets that are large and big
T/F sulfide bonds are highly stable and therefore require high energy to break
true
what does PDI stand for and its purpose?
Protein Disulfide Isomerase and it rearranges the polypeptides non-native S-S bonds
T/F: when proteins arise from the ribosome, they form by themselves and have errors ie disulfide bridges in wrong places. So PDI aids via -SH group
true
PPI helps via
helps to form proper configuration
HSP 70 and 40 require _
energy (ATP)
HSP 70 and 40 function to _
reverse misfolds, refolding, disaggregation, degradation
HSP 90 is for _
signal transduction proteins; integrates signaling functions acting at a late stage of folding substrates
mitochondria contain their own HSP 60 and 70 that are distinct and thus have their own _
quality control sys
interchain means
disulfide bond in btwn 2 chains ex bovine insulin
intrachain means
disulfide bond in same sequence
why is protein folding “all or none”
either folded or unfolded. Partially folded = toxic and diseases
why is molten globule the rescue step?
an intermediate and very short. Makes sure groups are finding each other and low energy state
4’ structure =
spatial arrangement of subunits and nature of their interactions
how do 3’ and 4’ structure differ?
3’ = 1 unit whereas 4’ = multiple subunits
all proteins have _ structure but only have some _ strucutre
all have 3’ and only some have 4’ structure
what are the 3 ways to denature proteins?
physical, chemical, and methods of analysis
denaturation means
damaging the protein’s structure
physical denaturation includes
Heat: making stable to unstable
pH (extremes) and agitation: both allow for aggregation
chemical denaturation includes
Detergent: SDS
Chaotropic agents: urea, guanidine hydrochloride (these interact with hydrophobic groups and messes with non-covalent bonds)
AND
Organic solvents: TCA (disrupts H bonds)
methods of analysis denaturation includes:
Turbidity (more hazy=more denatured) Circular dichroism (lt/rt polarize light differently) UV absorption (280nm) Fluorescence (inherited structures ie aromatic absorb light and emit) Biological activity (receptor proteins bind ligands strongly/lightly
molecular chaperons aid via
help proteins go into transient molten state
the 2 major classes of chaperones are:
HSP 70 and 90
and Chaperonins=a protein folding container (HSP 60 and 10)
T/F: every protein has a lifespan
true
Why must the cell remove aged and or damage proteins?
It’s better to recycle, but pathological diseases are associated with protein aggregation
what is the proteosome?
protein degradation machinery, large protease complex, and digests ubiquinated tagged proteins
in the 26S proteosome, which is the regulatory region and which is the catalytic core region?
19S
20S
19S
the 19S are the regulatory region and 20S is the catalyitc core
where do free aas come from and what can it be used for?
free aas come from peptide fragments of ubiquinated proteins. Free aas can be used for biosynthetic rxns.
