Protein Structure and Function 2 (L4) Flashcards
native state
protein folds into the most stable position (lowest free energy)
why are proteins not always in their native states inside the cell?
- multiple stable conformations
- pH
- need chaperones for folding
- not enough space inside cell
purpose of chaperones/chaperonins
assist in protein folding - creates isolated compartment for protein to fold properly
chaperones
HSP
chaperonins
GroEL, GroES -> cylindrical macromolecular complex
Alzheimer’s disease
abnormal protein folding -> amyloid plaques that are insoluble protein aggregates
amyloidogenic vs. non-amyloidogenic protein products
amyloidogenic: A-beta-42 pieces aggregate w/ each other
non-amyloidogenic: A-beta-40 pieces that are relatively soluble (not a problem)
A-beta normal vs. pathologic
normal: usually have alpha helices
path: more beta sheets that are more hydrophobic - fall out of solution and aggregate -> amyloid plaque
two classical pathological hallmarks of Alzheimer’s
neurofibrillary tangles (protein aggregates inside neurons) and amyloid plaques
concept of specificity
does protein bind only one thing or does it bind many things
concept of affinity
how tightly a protein binds its substrate
relationship b/w kd and affinity
high kd -> more dissociation -> low affinity
low kd -> less dissociation -> high affinity
what is an example of binding that is usually very tight and specific?
antibody-antigen (complementarity-determining regions)
antibody generation in B cells
somatic recombination then somatic hypermutation
somatic recombination
different combinations for binding w/ particular antigens
somatic hypermutation
evolved a way to create new mutations:
- deamination
- mismatch w/ error prone DNA pol -> more new lesions
- activation-induced deaminase: base-excision repair w/ low fidelity DNA pol delta -> create more mutations that generate variety in antibodies to bind more antigens
function of enzymes
molecular catalysts - increase rxn rate by lowering Ea of transition state
how do chemical reactions change enzymes?
they do not change they permanently
active site
mediates biochemical reaction - contains catalytic site + binding pocket
Michaelis-Menton equation
Vo = (Vmax x [S]) / ([S] + Km)
what are two characteristics of enzymes by which they can be described?
Kcat and Km - useful for comparing different enzymes
Km
measure of the affinity of an E for it’s S
= [S] when Vo = Vmax/2
relationship b/w Km and affinity
high Km -> more dissociation -> low affinity
low Km -> less dissociation -> high affinity
Vmax
the fastest rate that a specific unit of enzyme can work theoretically
how do serine proteases bind their substrates?
- binding site has beta sheets to H-bond w/ peptide to be broken
- specificity binding pocket to recognize specific S
- catalytic triad: Ser, His, Asp
- utilizes Ser in active site for nucleophilic attack on S
role of His in serine protease active site
imidazole ring can pick up H and have positive charge (is pH dependent) so it pulls H off of hydroxyl of Ser
at what pH can serine proteases not function and why?
low pH because at these pH levels, the active site His cannot pull the proton from Ser
pH and enzyme activity/efficiency
due to specific aa’s in active site - if they have the wrong charge, rxn cannot proceed
how are proteins involved in maintaining cell structure?
microfilaments - actin
microtubules - alphabeta - tubulin dimer
intermediate filaments
how are proteins involved in signal transduction?
- act as molecular switches - active vs. inactive
- channel proteins
- can be receptors, ligands, and/or signal transducers
how is Shh signal transduction pathway turned on?
ligand binds receptor -> active form -> triggers events -> transcription occurs
what are some clinical manifestions of mutations in Shh?
polydactyly, cyclopia
non-covalent protein modifications
- GTP switch
2. calmodulin
what regulates GTPase?
GEF and GAP
GEF
guanine nucleotide exchange factor - activates GTPases by stimulating release of GDP to allow binding of GTP
GAP
GTPase activating protein - bind activated G proteins and stimulates GTPase activity - terminates signaling event
how do you turn proteins off?
protein degradation by proteolytic cleavage
what is proteolytic cleavage mediated by?
proteosome
ubiquitination
labels proteins to be degraded with a protein tag (ubiquitin) put onto a Lys residue
proteosome function
recognizes ubiquitin labels, binds to protein, hydrolyzes ATP to release ubiquitin, then core of proteosome chops protein into pieces
