Flashcards in 1-42 Mutations and Proteins Deck (23):
the ramachandran plot shows us
the possible dihedral angles that can be observed in a given amino acid sequence
forces that restrict the forms that a protein can take on
protein structure works to maximize favorable charge-charge pairings
satisfy all hydrogen bonds
maximize van der Waals interactions
arrange hydrophobic residues such that they are not interacting directly with water.
All of these forces restrict the forms the protein can take on, influencing its folding heavily.
Often contain stretches of hydrophobic residues and act as transmembrane domains.
Alternating hydrophobic/hydrophilic residues make them the secondary structure of choice for the proteins of Gram-negatives’ porins; the hydrophobic parts face the membrane, and the hydrophilic parts line the inside of the channel.
gram negative porin secondary structure
hydrophobic parts face membrane, hydrophilic line the channel
reverse (beta) turn
tight turns in protein
usually contains proline
found in any protein sequence with sharp turns, including multi-pass transmembrane proteins
referred to as "irregular structure".
frequently forms binding site for other proteins/substrate.
proteins can share similar scaffolding, different loops sequences give rise to different functions
motif found in homeodomains and other DNA binding proteins in all kingdoms of life
motif that binds DNA less strongly than helix-turn-helix.
many are used together by transcription factors to bind DNA
extremely stable domains found in fibrous proteins like myosin. also observed as DNA-binding domains in trancription factors.
problems with folding in vivo
while protein transitions between different intermediates, some intermediates have exposed hydrophobic residues that can interact with neighbors.
overcome with chaperone proteins which cover exposed hydrophobic regions and help folding happen more smoothly
used for small proteins
binds proteins and covers exposed hydrophobic patches during folding
for larger proteins
takes misfolded proteins into its hydrophobic cavity.
ATPase puts a tight cap on the cavity, which changes it's conformation and reveals charged residues lining the cavity
the protein quickly sequesters its hydrophobic regions within the protein structure
uses atp to disassemble harmful protein aggregates
role of h-60 and hp70 is mainly to
prevent interactions that cause misfolding or aggregating
triple A domain of HP100
uses ATP hydrolysis to thread protein into the cleavage center
proteins frequently get mutated in the...
mitochondria - lots of oxidative damage
how to treat CF and alzheimers?
enhance ATP rate to stimulate chaperaones
inhibit chaperones. cancer tends to overexpress chaperones
protein degredation is regulated by..
ubiquitin/proeasome pathway. subunit will bind, eventually 4 wil link and signal cell degredation. uses enzyme ascade of e1, e2, 3e3.
4 ubiquitin attach, moves to proteosome
three parts of proteosome
most proteins are degreaded by the..