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BIOCHEM Exam 1 > Agbas Review > Flashcards

Agbas Review Flashcards

1
Q

2 types of interactions that govern protein folding stability

A

Non-covalent and hydrophobic

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2
Q

What are considered determinants of protein folding

A

Secondary structure, hierarchical folding, hydrophobic effect, context depending

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3
Q

How are alpha helix stabalized

A

Intrachain hydrogen bonds

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4
Q

In alpha helices what occurs between NH and C=O groups

A

Hydrogen bonds which stabilizes the helix

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5
Q

Where do the H bonds take place in an alpha helices

A

4 amino acid residues ahead in the sequence

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6
Q

How do amino acid residue relate to the next one in the chain

A

A rise of 1.5 A along the helix axis, 100 degrees rotation, 3.6 amino acid residues per turn

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7
Q

Which direction are most helices turning in nature

A

Right handed, it is more energetically favorable

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8
Q

How are beta sheets stabilized

A

H bonding between polypeptide strands

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9
Q

What are beta sheets composed of

A

2 or more polypeptide strands called beta strands which are fully extended

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10
Q

What is the distance between adjacent amino acids along a beta-strand

A

3.5 angstroms

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11
Q

Which protein folding motif can be found running parallel and antiparallel directions

A

Beta sheets

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12
Q

What is a reversal in direction in the structure of the protein called

A

Reverse turn, beta-turn, hairpin turn

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13
Q

T/F Loops have a regular periodic structure

A

False, loops do not have a regular periodic structure

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14
Q

What are 4 characteristics of polypeptide loops

A

Often well defined and rigid, Positioned on the surface of the protein, participates in protein-protein interactions, participates in interactions with other molecules

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15
Q

What is the timeline of proteins entering a folding funnel

A
  1. Rapid formation of secondary structure
  2. Formation of domains through cooperative aggregation
  3. Formation of assembled domains (molten globule)
  4. Adjustment of conformation
  5. More rigid structure
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16
Q

Characteristics of Molten Globule state

A
  1. 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 radios 10-30% larger than that of the native state
  4. The presence of a loosely packed hydrophobic surface area accessible to solvent
  5. It is no specific and occurs in early stage of protein folding
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17
Q

What is the function of protein disulfide isomerase

A

Rearranges the polypeptide non-native S-S bonds

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18
Q

T/F Molten Globule stage is intermediate and very short

A

True

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19
Q

T/F Partially loss of folding stabilizes the remainder of the structure

A

False, destabilized

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20
Q

T/F Protein folding can be partially completed

A

False, it is an all or nothing process

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21
Q

What is the function of HSP 70

A

Driven by ATP: Reverses misfolds, newly synthesized proteins, unfold/refold of trafficked proteins

22
Q

What is a molecular chaperone

A

Essential protein that binds to unfolded and partially folded polypeptide chains

23
Q

What does a molecular chaperone prevent

A

Improper association of exposed hydrophobic segments, non-native folding, polypeptide aggregation and precipitation

24
Q

What does molecular chaperone allow

A

Misfolded proteins to refold into native confirmation

25
Q

What do HSP 40 and 70 target

A

HSP 40 ubiquinates misfolded proteins HSP 70 escorts the ubiquitinated protein to the proteasome

26
Q

What occurs at the proteasome

A

Ubiquitinated proteins are processed to peptide fragments

27
Q

What happens to peptide fragments once they leave the proteasome

A

Further digested into free amino acids

28
Q

Can free amino acids be used for biosynthetic reaction following peptide fragment digestion

A

Yes

29
Q

What are the 3 cellular quality control systems discussed in the lectures

A

Proteasomes, autophagy, ERAD

30
Q

What does ERAD stand for

A

ER- associated degradation

31
Q

What are some of the problems involved with protein folding misteps

A

Improper degradation, improper localization, dominant negative mutation, gain of toxic function, amyloid accumulation

32
Q

What diseases is discussed in regards to improper protein degradation

A

Cystic fibrosis and gaucher’s disease

33
Q

T/F Overactive cellular degradation does not contribute to the accumulation of mutant, misfolded, incomplete degraded proteins

A

False, it does contribute

34
Q

What can lead to proteins being sent to the wrong location

A

Misfolding

35
Q

What can be caused by improper subcellular localization of proteins

A

Loss of function, gain of toxic function

36
Q

What is an Amyloid fiber

A

Insoluble protein aggregate

37
Q

What diseases are associated with amyloid accumulation

A

Alzheimer’s, Parkinson’s, Type 2 diabetes, Cataracts

38
Q

What does amyloidogenic disrupt

A

Cell membrane integrity

39
Q

What is the order of events that leads to amyloid plaques and what type of modifications enhance the formation of amyloid fibers

A

Seeding (nucleation), Fibril formation, deposit: Covalent modifications

40
Q

What are the keystones for environmental stressors

A

Detect, respond, adopt

41
Q

What does intrinsic induction of stress defense programs result in and what does it increase

A

Adaptation, life expectancy

42
Q

What does cellular and organismal functionality require

A

Protein production, folding, degradation

43
Q

What are the different pathways that ensure proteostasis and in which compartments do they take place

A

HSR (cytosol), UPRer (ER), UPRmt (Mitochondria)

44
Q

What does UPR stand for

A

Unfolded protein response

45
Q

What is the last line of defense for a cell in regards to misfolded proteins

A

Apoptotic pathway

46
Q

What do Heat shock protein manage

A

Denatured proteins in the cytosol

47
Q

What is the effect of UPRer

A

Increase protein chaperones, increase rate of ERAD, decrease protein production, finally apoptosis as a last line of defense

48
Q

What is the most recently discovered UPR

A

Mitochondrial

49
Q

Where is UPRmt encoded

A

In both nuclear and mitochondrial DNA

50
Q

How many essential proteins of the ETC are encoded by mtDNA

A

13

51
Q

What are the 2 major mitochondrial chaperon system

A

mtHSP 70, Multimeric HSP60-HSP-10 machinery in the mitochondrial matrix

BIOCHEM Exam 1 (5 decks)

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