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biomedical biochemistry > protein targeting > Flashcards

protein targeting Flashcards

1
Q

what are the four levels of protein structure?

A

primary
secondary
tertiary
quaternary

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2
Q

which pathway are sulfide bonds found in?

A

secretory

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3
Q

what is the definition of native structure?

A

the folded, active form of a protein

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4
Q

what is the definition of random coil?

A

the unfolded structure with no secondary structure

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5
Q

what is the definition of conformation?

A

a change in the 3D structure through rotation of bonds

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6
Q

what is the definition of denaturation?

A

destruction of native structure by a change of conformation

can return to active conformation

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7
Q

what is the definition of degradation?

A

breaking of covalent bonds to from smaller molecules

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8
Q

what is protein homeostasis?

A

ensuring there is the correct amount of functional protein at all times

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9
Q

what is protein homeostasis governed by?

A

production
folding
trafficking
degradation

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10
Q

what are possible destinations for proteins?

A

stay in the cytosol
mitochondria or nucleus (post translational trafficking)
secretory pathway (co translational trafficking)

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11
Q

what is the basic secretory pathway?

A 
ER
cis golgi 
golgi 
trans golgi 
secretory vesicle 
plasma membrane
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12
Q

what are common features of ER sorted protein signal sequences?

A

have between 13-36 amino acids leading the protein
contain 10-15 hydrophobic amino acid sequences
a short polar sequence at the carboxyl terminus

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13
Q

what is the role of chaperones during translation?

A

Hsp70
stabilise unfolded protein
associate with hydrophobic residues to prevent misfolding or aggregation

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14
Q

what is the role of chaperonin?

A

provides an isolated environment in which correct folding can occur
shields the polypeptide from the cytosol and prevents aggregation
used for proteins which are difficult to fold

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15
Q

what is the role of cytosolic chaperones during post translational trafficking?

A

transport partially folded polypeptides from cytosol to mitochondria
stabilises unfolded polypeptide

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16
Q

what is the role of mitochondrial chaperones?

A

facilitate transport and folding of polypeptide within the organelle

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17
Q

how are proteins targeted to the ER?

A

signal recognition particle (SRP) recognises signal sequence and binds to N terminal of translated protein as it emerges from the ribosome
translation is halted
SRP escorts the complex to the ER where it binds to a SRP receptor
SRP is released, the ribosome binds to the translocon and the signal sequence is inserted
translation resumes
signal sequence is cleaved
growing polypeptide chain is translocated across the membrane and released into the ER lumen when completed

18
Q

what cleaves the signal sequences in the ER?

A

signal peptidase

19
Q

what mediates protein folding in the ER?

A

BiP

20
Q

what is sulphide bonding mediated by and what is it promoted by?

A

mediated by protein disulphide isomerase

promoted by oxidising environment in ER lumen

21
Q

what is N-linked glycosylation?

A

the addition of N-acetylglucosamine to asparagine

22
Q

what is O-linked glycosylation?

A

the addition of N-acetylgalactosamine to serine

23
Q

what happens during glycosylation in the ER?

A

a 14 sugar oligosaccharide is first synthesised on dolichol in the ER membrane
then transferred to the consensus sequence on an asparagine residue
3 glucose residues are removed

24
Q

how many enzymes does the golgi apparatus contain and what do they catalyse?

A

over 250 enzymes

catalyse addition of sugars to proteins

25
Q

where are proteins which contain mannose-6-phosphate transported to?

A

endosomes

26
Q

what happens in post golgi transport?

A

proteins in the trans-Golgi network are sorted into vesicles and then transported to final destination
also sorted into secretory granules
secretory granules store their contents until specific signals direct their fusion with the plasma membrane

27
Q

how many proteins does the mitochondrial genome encode for?

A

13

28
Q

why does the protein need to be in a partially unfolded when being transported to the mitochondria?

A

mitochondrial translocons are quite small

29
Q

what is the TOM complex?

A

translocase of the outer membrane

30
Q

what is the TIM complex?

A

translocase of the inner membrane

31
Q

how are mitochondrial proteins with presequences imported into the mitochondria?

A

N-terminal presequences target the protein to the TOM complex
after translocation through TOM the presequence binds to TIM complex
Hsp70-containing import motor complex in the matrix drives translocation across the inner membrane
proteins with internal transmembrane domains exit TIM laterally
proteins destined for the matrix associate with chaperones and presequences are cleaved by mitochondrial matrix processing peptidase

32
Q

how are proteins targeted to the mitochondrial inner membrane?

A

inner membrane protein with transmembrane domains have internal signal sequences
after translocation through TOM the polypeptide associates with TIM9-TIM10 chaperones in the intramembrane space which transfer the protein to the TIM complex
internal membrane sequence halts translocation and the protein exits the translocon laterally into the inner membrane

33
Q

what are proteins which are encoded by the mitochondrial ribosomes translocated via?

A

Oxa1 translocase

34
Q

what are alpha helical transmembrane domain proteins which are destined for the outer mitochondrial membrane inserted by?

A

Mim1

mitochondrial insertase

35
Q

how are beta barrel precursors inserted into the outer mitochondrial membrane?

A

transferred through TOM and carried to SAM by TIM chaperones and is inserted into the outer membrane

36
Q

what are NLS and what are they recognised by?

A

nuclear localisation signals

recognised by importins

37
Q

what are NES and what are they recognised by?

A

nuclear export signals

recognised by exportins

38
Q

are nuclear localisation signals cleaved?

A

no

39
Q

what is the directionality of transport across the nuclear pore determined by?

A

Ran

a GTP-binding protein

40
Q

how are proteins transported into the nucleus?

A

transport begins when NLS is recognised by an importin
cargo/importin complex binds to nuclear pore protein and is transported through the pore
in the nucleus, Ran/GTP binds importin and the cargo protein is released
importin-Ran/GTP is re-exported through the pore
Ran-GDP associates with NTF2 and Ran-GEF exchanges GDP for GTP

biomedical biochemistry (7 decks)

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