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BIOL 200 > KH4 > Flashcards

KH4 Flashcards

1
Q

What is the structure of properly folded proteins

A

Hydrophobic amino acid side chains are not exposed at the surface but are buried in the core

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2
Q

What is a general sign of misfiling

A

Hydrophobic patches at the surface of a protein

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3
Q

What does in vitro conversion between native and denatured conformations show

A

Native conformation can be denatured (with urea) and renatured which shows that 3D structure is determined by amino acid sequence

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4
Q

Characteristics of misfiled proteins

A
  • wrong conformation
  • Insoluble
  • Aggregation irreversible
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5
Q

Which region folds first N or C terminus

A

N-terminus

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6
Q

How is spontaneous refilling of a denatured protein through t to be through

A

A folding pathway

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7
Q

What are chaperones and what are their functions

A

Proteins that help guide protein folding along productive pathways by permitting partially misfolded proteins to return to the proper folding pathway

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8
Q

Where can chaperones be upregulated

A

Under conditions where misfolded proteins accumulate (ex: heat shock induced proteins)

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9
Q

What are examples of functions of chaperones

A
  1. Can fold newly made proteins into functional conformations
  2. Refold misfolded or unfolded proteins into functional conformations
  3. Disassemble potentially toxic protein aggregates that form due to protein misfolding
  4. Assemble and disassemble large multi protein complexes
  5. Mediate transformations between inactive and active forms of some proteins (changing shape)
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10
Q

How do chaperones work

A

Work through ATP-dependent cycles of binding to, and release from misfolded client molecules at exposed hydrophobic patches

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11
Q

How does blocking the exposed hydrophobic patches help

A

The chaperones can keep folding or refolding protein out of trouble while productive folding events occur (protect from aggregation until properly folded)

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12
Q

What are the two major classes of chaperones

A
  1. Molecular chaperones (operate as single molecules)
  2. Chaperonins (form a multi subunit refolding chamber)
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13
Q

Structure of chaperonins

A

Form and enclosed chamber made up of inward-facing protein binding subunits that undergo concerted ATP-binding/hydrolysis and conformation change

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14
Q

How many proteins make up the quaternary structure of chaperonins

A

7 with a chamber inside (where refolding occurs)

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15
Q

What are the groups of chaperonins

A

Group 1: removable cap
Group 2: no removable cap, lip and conformational change

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16
Q

Why are chaperonins/chaperones essential to life

A

The majority of cellular proteins require the assistance of chaperonins/chaperones to adopt their 3D structures during synthesis or to properly refold if misfolded

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17
Q

Chaperonin/chaperone evolution characteristics

A

Ancient, very highly conserved in amino acid sequence through evolution

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18
Q

What happens w=if chaperones/chaperonins can’t correct the misfolding

A

Proteins are destroyed by proteolytic cleavage into small fragments

19
Q

What are chaperones most likely to recognize

A

Exposed hydrophobic patches

20
Q

What are the steps for ubiquitin/proteasome system for protein degradation

A

Step 1: Poly-ubiquitin tags damaged or misfolded proteins for degradation
Step 2: Ubiquitin-tagged proteins are fed into a multi subunit chamber in which the subunits form inward-facing proteases

21
Q

What is ubiquitin and what can it do

A

A 76-residue protein that can be covalently linked to lysine residues on target proteins

22
Q

What compounds are involved in step 1 of the ubiquitin/proteasome system for protein degradation

A

E1: ubiquitin activating enzyme
E2: Ubiquitin-conjugating enzyme
E3: Ubiquitin ligand
Ubiquitin

23
Q

What is the function of E1 and E2

A

Takes ubiquitin, hydrolyzes ATP and uses energy to attach ub to itself on C-terminal

24
Q

What is the function of E3

A

Recognizes the protein that should be destroyed, targets misfolded proteins (recognize exposed hydrophobic patches)

25
Q

How does E3 recognize and target for degradation of normal proteins that the cell needs to degrade for regulatory purposes (cyclins)

A

E3 recognition of cyclins is triggered by their regulated phosphorylation at a specific amino acid residue

26
Q

What can proteins in a proteasome cap do

A
  1. Recognize and bind poluubiquitin
  2. Remove targeting ubiquitin by hydrolysis
  3. Unfold target proteins (using energy from ATP)
  4. Feed target proteins into central chamber of 20S core
27
Q

What does the 20S core subunits of a proteasome do

A

Forms inward-facing proteases that degrade proteins to amino acids or short oligopeptides

28
Q

What does the overall design of the proteasome do

A

Isolates the active proteases from the cytoplasm minimizing the dangers of an enzyme that destroys proteins

29
Q

What happens when protein quality control (proteasomes) fails

A

Accumulation of aggregates of insoluble proteins (could take a long time)

30
Q

What are the steps a protein may go through before becoming a protein aggregate

A
  1. Correctly folding without help
  2. Correctly folding with the help of a chaperone
  3. Incompletely folded forms digested in proteasome
31
Q

What is an amyloid

A

An accumulation of misfolded proteins that is an important aspect of several neurodegenerative disease (visible as plaques or tangles)

32
Q

What does an amyloid precursor turn into after being cleaved into alpha helices and beta sheets

A

An aggregation into filaments resistant to proteolysis

33
Q

Common neurodegenerative diseases are associated with what

A

Accumulation late in life of insoluble and presumably toxic misfolded proteins aggregates

34
Q

What happens to most proteins after they are denatured and urea has been removed

A

They aggregate

35
Q

Why are chaperones known as heat shock proteins

A

Because heat denatures proteins and encourages misfolding so chaperones will flock there

36
Q

What is the binding between an unfolded protein and a chaperone

A

Not strong in open conformation, strong in closed conformation

37
Q

How does a chaperone go from open to closed conformation

A

ATP hydrolysis and a change in conformation

38
Q

How does a chaperone go from closed to open

A

ATP replaces released ADP + Pi

39
Q

Difference between chaperonins in bacteria vs eukaryotic cells

A

Eukaryotic chaperonins have no cap, they close by changing conformation

40
Q

What is the rage for a proteasome

A

The ubiquitin chain on the misfolded protein

41
Q

What does E1 do in the ubiquitin/proteasome system

A

Links c terminus of ubiquitin to itself with a covalent bond and hydrolyzes ATP to AMP

42
Q

What does a cytosolic target protein have

A

An amino group on lysine (misfolded)

43
Q

What is an isopeptide bond and how does it differ from a peptide bond

A

It is between the Ub and side chain of lysine, identical to a peptide bond except it’s not on a backbone

44
Q

What happens to misfolded proteins once in the proteasome

A

ATPases I fold protein and run it down centre chamber where the poly ubiquitin chain is chopped off of the target protein

BIOL 200 (13 decks)

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