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Biochemistry > Protein Folding Review > Flashcards

Protein Folding Review Flashcards

1
Q

interactions that govern protein folding stability

A

non-covalent

hydrophobic

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2
Q

non-covalent interactions

A

Van der Waals interactions (short range repulsion)

hydrogen bonds

electrostatic forces (e.g. ion pairs and salt bridges)

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3
Q

hydrophobic interactions

A

nonpolar groups do not interact favorably with water

their favorable interactions are primarily the results of their exclusion from water

the hydrophobic interaction is a major factor in the folding and stability

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4
Q

determinants of folding

A

secondary structure (for an efficient packing)

hierarchical folding

hydrophobic effect

context dependent

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5
Q

alpha helix is stabilized by intrachain hydrogen bonds between the _____ and ______ groups

A

NH

C=O

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6
Q

hydrogen bonds in alpha helix form _____ amino acid residues ahead in the sequence

A

4

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7
Q

alpha helices can be right (clockwise) and left handed, alpha helices found in proteins are _____ - handed because they are energetically more favorable

A

right

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8
Q

beta sheets are stabilized by hydrogen bonding between _______ strands

A

polypeptide

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9
Q

a beta sheet is formed by linking

A

2 or more beta strands via hydrogen bonds

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10
Q

beta sheets can run in

A

parallel or antiparallel direction

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11
Q

reversal directions in polypeptide chain provides

A

compact and globular shapes for polypeptide chain; they’re called reverse turn, beta turn, and hairpin turn

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12
Q

in many reverse turns, C=O and N-H groups form

A

hydrogen bonds for stability

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13
Q

loops do not have regular periodic structure, they are often ______ ; positioned ______ ; and participate in ______ and ______

A

well defined and rigid

on the surface of the protein

protein-protein interactions and interactions with other molecules

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14
Q

heptad repeat

A

a type of random repeat sequence in which a group of 7 amino acids occurs many times in a protein sequence

often found in superhelix

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15
Q

folding funnel steps

A
  1. rapid formation of secondary structures
  2. formation of domains through cooperative aggregation (concept of folding nuclei)
  3. formation of assembled domains (concept of molten globule)
  4. adjustment of conformation
  5. more rigid structure
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16
Q

molten globule state charactersitics

A
  1. the presence of a native-like content of secondary structure
  2. the absence of a specific tertiary structure produced by the tight packing of amino acid side chains
  3. compactness in the overall shape of the protein molecule, with a radius 10-30 percent larger than that of the native state
  4. the presence of a loosely packed hydrophobic core that increases the hydrophobic surface area accessible to solvent
  5. it is not specific and occurs in early stage of protein folding
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17
Q

tertiary structure

A

spatial arrangement of amino acid residues that are far apart in the sequence and to the pattern of disulfide (S-S) bonds

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18
Q

protein disulfide isomerase (PDI)

A

rearranges the polypeptide’s non-native S-S bonds

fixes incorrect disulfide bonds

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19
Q

protein folding is a highly ______ process

A

cooperative

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20
Q

proteins can be denatured by several treatments to disrupt

A

the tertiary structure

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21
Q

protein folding and unfolding in a ______ process

A

all or none

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22
Q

molten globule stage is ______ and ______

A

intermediate

very short

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23
Q

partially loss of folding destabilizes the

A

remainder of the structure

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24
Q

quaternary structure

A

spatial arrangement of subunitS and nature of their interaction

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25
Q

PPI (peptidyl prolyl cis-trans isomerase)

A

assists with cis-trans transition

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26
Q

mitochondria contain their own _____ and _____ molecules that are distinct from those that function in the cytosol

A

Hsp60

Hsp70

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27
Q

functions of molecular chaperons Hsp70/40

A

ATP-driven

reverses misfolds; assists with newly synthesized proteins; unfold/refold of trafficked proteins

28
Q

chaperonins are a subtype type

A

chapernons

29
Q

molecular chaperon functions

A
  1. essential proteins that bind to unfolded and partially folded polypeptide chains
  2. they prevent the improper association of exposed hydrophobic segment
  3. non-native folding, polypeptide aggregation, and precipitation will not occur
  4. they allow misfolded proteins to refold into their native conformation
30
Q

native protein –> soluble –> _______ tries to refold, if not it ubiquinates and _____ assists with proteasoe

A

Hsp40

Hsp70

31
Q

native protein –> insoluble –> ______ and ______ ubiquinate and send to proteasome

A

Hsp40

Hsp70

32
Q

ubiquitinated proteins are processed to ______ ; which are further processed to yield ______ ; these can can used for

A

peptide fragments

free amino acids

biosynthetic rxns

33
Q

what structures or processes are involved in cellular quality control system

A

proteasomes

autophagy

ERAD (ER-Associated Degradation)

34
Q

how does protein-folding cause diseases?

improper degradation

A

overactive cellular degradation systems (ERAD, autophagy) can contribute to the accumulation of mutant, misfolded, incomplete degraded proteins

this improper degradation of proteins can contribute to the development of more severe diseases

e.g. cystic fibrosis

35
Q

how does protein-folding cause diseases?

improper localization

A

for proper trafficking to target organelles, proteins must fold correctly

incorrectly folded proteins lead to improper subcellular localization (resulting in loss-of-function: protein isn’t transported correctly to target organ so target organ cannot function properly or gain-of-function: protein isn’t able to be transported out of original organ and causes dysfunction in organ where it was synthesized)

e.g. AAT

36
Q

how does protein-folding cause diseases?

dominant negative mutation

A

a mutant protein antagonizes the function of the wild-type protein leading to: loss of protein activity; and mutant protein presence interferes with function of the WT protein at cellular and structural levels

e.g. p53

37
Q

how does protein-folding cause diseases?

gain-of-toxic function

A

protein conformational changes can cause dominant phenotypes

e.g. ApoE in Alzheimer’s disease; Src kinases in cancer

38
Q

how does protein-folding cause diseases?

amyloid accumulation

A

e.g. cataracts and alzhiemer’s disease

39
Q

amyloid fibers

A

insoluble protein aggregates

40
Q

amyloidogenic proteins have ______ sequence

A

VQIVY

41
Q

lower order oligomers cause

A

toxic effect

42
Q

amyloid deposits could be a

A

protective mechanisms

43
Q

several amyloidogenic proteins from pore-like structures that

A

disrupts the cell membrane integrity

44
Q

misfolded forms of the protein are frequently observed in

A

the elderly as part of the natural aging process

individuals with mutations in the protein early in life

45
Q

how do amyloid fibers progress to amyloid plaques

A

seeding (nucleation) –> fibril formation –> deposit

46
Q

keystones for environmental stress

A

to detect

to respond

to adopt

47
Q

intrinsic induction of stress defense programs and resulting adaptation can

A

increase life expectancy

48
Q

proteostasis

A

maintenance of protein homeostasis

49
Q

cellular and organismal functionality requires

A

protein production

folding

degradation

50
Q

complex pathways to ensure proteostasis in different compartments include

A

cytosol (Heat Shock Response)

ER (UPRer)

Mitochondria (UPRmt)

51
Q

cellular proteins are folded

A

by chaperons

52
Q

membrane and secreted proteins fold and mature where

A

in the ER

53
Q

what is the last line of defense in regards to maintaining proteostasis

A

apoptotic pathway

54
Q

heat shock response (HSR) manages denatured proteins in

A

the cytosol

55
Q

unfolded protein response ER (UPRer)

A

unfolded or misfolded proteins accumulate in ER causing ER stress

ER stress initiates a single pathway called unfolded protein response (UPR)

this pathway is intended to save the cell

56
Q

functions of UPRer

A

increase protein chaperones

increase rate of ERAD

decrease protein production

last resort is apoptosis

57
Q

steps of autophagy

A

isolation membrane formation

identification and collection of cellular components for degradation

completion of autophagosome

fusion of autophagosomoe with lysosome

formation of autolysosome and degradation of contents

58
Q

steps of ERAD

A

translocation into ER

degradation of misfolded proteins through translocation out of ER and into proteasome

59
Q

which UPR pathway is most recently discovered

A

UPRmt

60
Q

mitochondrial proteome is composed of how many proteins

A

1500

61
Q

mitochondria proteins are encoded by

A

nuclear and mitochondrial genome

62
Q

13 essential proteins of ______ are encoded by mtDNA

A

ETC

63
Q

what are the 2 major mitochondrial chaperon systems

A

mtHSP70

multimeric HSP60-HSP10 machinery in the matrix

64
Q

UPRmt protein quality control (PQC) proteases:

A

are specific for each mitochondrial compartment

recognize and degrade the proteins that don’t fold and that aren’t properly assembled

65
Q

if the UPRmt senses the overload of the QC (quality control) system, it

A

activates the transcription of nuclear encoded protective genes by retrograde signaling

re-establishes the mitochondrial homeostasis

Biochemistry (32 decks)

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