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47 Cards in this Set

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protein folding is driven by a number of ... interactions such as hydrogen bonding, ionic interactions, Van Der Waals' forces and hydrophobic packing.
noncovalent
which structure is this?
-linear sequence of amino acids held together by peptide bonds (dictated by the gene encoding that particular peptide or protein)
-all other aspects of protein structure are derived directly from this structure (or sequence) or the protein!
primary structure
which structure is this?
-repeating structural elements produced through the hydrogen bonding of molecules in the peptide backbone itself.
secondary structure
what are the 2 main forms of secondary structure?
alpha-helix and beta-sheet
... (amino acid) is often found at the beginning of alpha helices, and ... is often found at the ends.
proline
glycine
which type of secondary structure has intra-strand hydrogen bond formation?
alpha-helix
which structure is this?
-the folding pattern of the secondary structural elements into a 3-D conformation
-designed to serve all aspects of the protein's function (binding sites, cellular localization, catalytic sites)
tertiary structure
protein folding is what converts a polypeptide linear chain of amino acids into a specific 3-D structure.
The process begins ..., so N-terminus begins to fold while C-terminus is still being synthesized by ribosome
co-translationally
protein folding results from chemical properties of individual amino acids in the ... structure of the protein
primary
amino acid side chain ... result in protein folding
interactions
... and ... groups of the peptide backbone maximize their potential to form hydrogen bonds with other backbone atims
amide
carboxyl
elements of ... structure usually extend completely across compact domains
secondary
protein folding is aided by a class of cellular proteins known as ... or ... proteins
chaperones
heat shock proteins
chaperones use energy provided by ... to assist in folding of newly synthesized protein chains.
ATP
2 examples of chaperone proteins are ... and ...
Hsp70 (Bip)
Hsp60 (GroEL/GroES)
heat shock proteins that aid in protein folding belong to ... family
chaperonin
Hsp70 is located in the ... and is associated with ribosomes as the protein is forming. It stabilizes the chain until it's at the proper length to fold.
ER
Hsp60 is located in the ...
mitochondria
the protein waits to fold until it gets into the ...

This is so that we don't activate the protein early.
mitochondria
Heat shock proteins stop hydrophobic regions from ...
aggregating
The other 2 proteins involved in folding and are found in the RER are ...
cis-trans isomerases

protein disulfide isomerases (PDI)
cis-trans isomerases change peptide bond configuration. Changes any ... bonds into ...

the exception would be ... (AA)
cis
trans
proline
protein disulfide isomerases form disulfide bonds.

ex. 2 ...(AA) form a crosslink
cysteines
what is this?
-abnormal accumulation (and resulting toxicity) of proteins in certain disease states
-also known as protein conformational disease
-caused by changes in protein folding that increase the tendency of the protein to misfold and polymerize into aggregates that are resistant to clearance and can become pathogenic
proteopathy
Risk factors for proteopathy:
-almost always involves in increase in ... secondary structure
-destabilizing changes in primary amino acid sequence of protein (...)
-abnormal ...
-changes in ... and ...
-increase in ...
-decrease in ...
-advancing ...
-beta sheet (tend to clump more than alpha helices)
-mutations
-post-translational modifications
-temperature and pH
-protein production
-protein clearance
-age
These are examples of what?
-alzheimer's disease, prion disease, parkinson's disease, huntingon's disease, type II diabetes, etc.
proteopathy
quaternary structure is present in proteins with ...
multiple subunits
in quaternary structure, interaction between ... may involve hydrogen binding, hydrophobic interactions, or covalent binding in the form of disulfide bonds
individual polypeptide chains
the 3 advantages of quaternary structure are ...
increased stability
cooperative binding
high affinity binding
an example of a molecule in quaternary structure that exhibits positive cooperativity is ...
hemoglobin
-Hemoglobin S and sickle cells are caused by a single change in amino acid sequence (...-->...) in the 6th position of the beta chains.
-leads to changes in ...(now they tend to aggregate) and ...(affinity for O2 has been lowered)
Glu-->Val
solubility
function
In someone with sickle cell anemia, what is it called when the hemoglobin cells clump together and the blood can't travel? It occurs during times of overexertion and stress.
sickle cell crisis
the sickle cell trait seems to have evolved to protect from ...
malaria
Immunoglobulins consist of 2 ...chains and 2 ... chains. Their quaternary structure leads to the function of binding to a specific antigen
light
heavy
an example of fibrous protein is ...
keratin
a keratin alpha helix joins with another one to form a ..., which then combines again to form a ..., and then again to form a ...
two-chain coiled coil
protofilament
protofibril
keratin is high in which 2 amino acids? (they are the smallest amino acids)
glycine and alanine
keratin contains 14% of which amino acid? Because of this, it has a high capacity to disulfide bond.
Cysteine
what are the levels of keratin in the cross section of a hair? (starting with alpha helix and ending with cells)
alpha helix, two-chain coiled coil, protofilament, protofibril, intermediate filament, cells
to perm hair, you use a ... agent, a base like ammonium hydroxide and ammonium thioglycolate in order to break the disulfide bonds. Then you curl. And when you want to reform the new disulfide bonds, you use an ... agent, a neutralizer like hydrogen peroxide
reducing
oxidizing
when a protein unfolds, or ..., it loses its 3-D shape and its function.
denatures
what are 5 causes of protein denaturation?
-nonenzymatic modification (glycosylation, oxidation)
-high temperature
-high concentrations of urea
-extremes of pH
-solvents that disrupt ionic, hydrogen, and hydrophobic bonds
thermal denaturation:
-enzymes and other proteins will begin denaturing at temperatures between ...
-most of the time, our ... regulates our body temp so that these temps are never reached (except in cases of severe infections or dangerously high fevers)
-in fried eggs, denatured albumin forms a ...
-
104 and 106 degrees F
hypothalamus
white precipitate
We must maintain the proper temperature, otherwise proteins may begin to ... and lose their ...
unfold
function
... of hemoglobin can result in protein denaturation. This can be caused by sustained high glucose levels (...)
glycosylation
hyperglycemia
a glycosylated hemoglobin is also known as ...
-this serves as a valuable indicator of blood glucose levels over an extended period of time and is used to monitor how successfully a diabetic's blood sugar is being controlled.
HbA1c
glycosylation of hemoglobin doesn't affect ... of the protein in this case
function