BIOL408, Unit 1: protein structure and folding

what are the parts of an amino acid?

central carbon, amino group, carboxyl group, R group

primary structure

covalent peptide bonds

secondary structure

hydrogen bonds form shapes (alpha helix, beta pleated sheets)

tertiary structure

attractions between secondary structure

quaternary structure

exists in proteins with more than one amino acid chain

hydropathy plot

analyzes protein structure based on hydro-affinity

protein domains

tertiary structures in a protein that have specific structural or functional features

how does the protein folding environment in vivo differ from protein folding in vitro?

there are crowded conditions, degradation signals, higher temperatures, and simultaneous translation and folding

protein chaperones

aid in folding, unfolding, and transport of proteins, not necessary for folding

what are the main protein chaperones?

heat shock proteins

how does HSP70 compare to HSP60

70 is more common, 60 exist mainly in mitochondria

HSP70

stabilizes translating proteins, transport proteins, and fold and unfold proteins

where do chaperone proteins bind?

hydrophobic regions, prevents hydrophobic amino acids from binding before they are properly folded

HSP40

identifies proteins needing assistance from HSP70

what are reasons that proteins are degraded?

they are no longer needed, they were misfolded, or amino acids are needed for more critical purposes

why does denaturation occur?

changes in pH, salt concentration, or temperature

proteasome

complex of proteolytic domains

26s proteasome

main proteasome, contains 20s proteasome and 19s cap

which part of the 26s proteasome is ATP dependent?

the 19s cap

ubiquitin

76 amino acid protein that tags other proteins for degradation

how do the classes of ubiquitin enzymes differ?

they differ in function and quantity, fewest E1s, most E3

E1

Ub activating, ATP dependent

E2

Ub conjugating, carries ubiquitin to complex with E3

E3

Ub ligases, transfers ubiquitin with substrate protein

binding to K48

proteasome

binding to K63

signaling/autophagy

what are alternate degradation pathways?

lysosomes and autophagy

autophagy

when proteins are engulfed by autophagosomes and transported to lysosomes

what are the two kinds of autophagy?

bulk and selective

selective autophagy

specific substrates are ubiquitinated and engulfed by autophagosomes