Protein Folding, Misfolding, Aggregation, and Disease

Question 1

Can form aggregates that interfere with other cellular functions

Answer 1

Unfolded Proteins

Question 2

Regulatory mechanisms that promote correct folding are balanced by proteolytic pathways that degrade persistantly damaged

Answer 2

Proteins

Question 3

Increased levels of misfolded proteins can lead to a number of disease, including

Answer 3

Neurodegenerative conditions

Question 4

Can play a significant role in guiding the correct folding of the polypeptide chain, to generate the structural and catalytic properties of the protein

Answer 4

The sequence of amino acid residues

Question 5

While genetic mutations affect all the polypeptide chains produced from a specific mRNA, errors can also arise from inserting incorrect amino acid in the growing chain, and by slippage of the ribosome on the mRNA template resulting in

Answer 5

Frameshifting

Question 6

Can occur spontaneously, or be induced by environmental stresses

Answer 6

Post-translational misfolding

Question 7

Can occur co-translationally or post-translationally and can confer alternate biochemical fates

Answer 7

Protein folding

Question 8

What interactions promote protein folding?

Answer 8

1. ) Hydrophobic
2. ) Electrostatic
3. ) van der Waals
4. ) Disulfide bonds
5. ) Metal coordination

Question 9

What are some agents that promote unfolding?

Answer 9

Temperature, pH, pressure, urea, etc

Question 10

Key information for protein folding is present in the

Answer 10

Polypeptide sequence

Question 11

Based on a fundamental understanding of the physical and chemical properties of amino acids, proposed the formation of α-helices and β-sheets

Answer 11

Linus Pauling

Question 12

Showed that bovine pancreatic ribonuclease could be fully denatured by treatment with β-mercaptoethanol (β-Me reduces disulfide bonds) and 8M urea (which unfolds proteins by disrupting non-covalent interactions and solubilizing non-polar residues).

Answer 12

Anfinsen experiment

Question 13

In the Anfinsen experiment, rapid removal of β-Me and urea only allowed

Answer 13

1% of activity of protein to be recovered

Question 14

In the Anfinsen experiment, slow removal of β-Me and urea by step-wise dialysis restored

Answer 14

Almost full activity

Question 15

The conclusion from the Anfinsen experiment was that the information for generating the secondary and tertiary structure in a protein is intrinsically available in the

Answer 15

Polypeptide sequence

Question 16

All the information necessary to assemble and generate full enzymatic activity is present in the

Answer 16

Amino acid sequence

Question 17

Small proteins may fold rapidly and spontaneously, however, large proteins tend to require

Answer 17

Chaperones

Question 18

States that particular folding pathways must be favored by a specific protein because otherwise it would take too long for proteins to fold

Answer 18

Levinthal’s Paradox

Question 19

Do not enhance correct folding, rather they prevent non-productive routes

Answer 19

Molecular chaperones

Question 20

Posits that evolution has selected polypeptide chains in which the individual amino acids are positioned so that they maximize correct folding events, and minimize structural barriers (through their side chains).

Answer 20

Bryngelson and Wolynes Principal of Minimal Frustration

Question 21

Bryngelson and Wolynes Principal of Minimal Frustration basically says that the folding pathway for a polypeptide does not proceed in a

Answer 21

Linear manner

Question 22

The ΔG between unfolded and folded/native protein is very

Answer 22

Small

Question 23

The average stability per residue is

Answer 23

0.1 kcal/mole

Question 24

Can promote folding of specific proteins, or participate in general quality control mechanisms

Answer 24

Chaperone proteins

Question 25

Chaperone proteins that promote the folding of proteins emerging from the ribosome are likely to be

Answer 25

Non-specific

Question 26

Chaperone proteins that assist in the assembly of large multi-subunit complexes are typically

Answer 26

Highly specific to a particular task

Question 27

Has a significant impact on the global structure of the folded protein

Answer 27

Hydrophobic core

Question 28

Have a significant impact on the local environment of a folded protein

Answer 28

Electrostatic interactions and van der Waals interactions

Question 29

Have a significant impact on a folded proteins stability

Answer 29

Disulfide bonds

Question 30

Has a significant impact on the structure and stability of a folded protein

Answer 30

Metal coordination

Question 31

A common DNA binding domain present in many enzymes and nucleic acid binding proteins

Answer 31

Zinc Finger (RING motif)

Question 32

Water molecules around a hydrophobic protein structure are constrained because certain hydrogen bonds resist pointing towards the

Answer 32

Hydrophobic amino acid residues

Question 33

Larger proteins that achieve 3-D conformation with help from a chaperonetypically can not be

Answer 33

Renatured following denaturation

Question 34

Protein denaturation is not concentration dependent (zero order kinetics) and is simply a function of protein

Answer 34

Vulnerability to the denaturant

Question 35

The temperature at which 50% of the proteins molecules are unfolded -A measure of the thermodynamic stability of the protein

Answer 35

Transitional melting Temperature (Tm)

Question 36

The Tm can be affected by

Answer 36

Mutation, post-translational modification, and association with other proteins

Question 37

What are four agents that can promote folding?

Answer 37

Co-factors, disulfide bond, chaperones, and physiological partners

Question 38

Help to shield the hydrophobic cores of proteins until they are released from the ribosome and can fold into their final conformations

Answer 38

Molecular chaperones

Question 39

The chaperones stabilize the nascent chain, prevent deleterious interactions with other constituents in the cell, and provide an opportunity for the protein to achieve its

Answer 39

Mature structure

Question 40

Predicts that folding resembles a simple chain reaction with reactants and products -Each sub-step culminates in a folded intermediate that can then proceed into the next folding event

Answer 40

Sequential folding model

Question 41

The sequential folding model is improbable since

Answer 41

Intermediates have never been detected

Question 42

Posits that a polypeptide chain can enter multiple folding pathways, although only one path leads to a productive native structure

Answer 42

Continuum folding model

Question 43

A polypeptide chain that has achieved a near-final secondary structure (i.e. alpha helices & beta sheets), but is maintained in a less ordered 3-D structure that is 'looser' and more 'open' than the final structure

Answer 43

Molten Globule

Question 44

Not a defined structure, but refers to a family of related structures that are fluid and interchangeable -Can be represented as U M N

Answer 44

Molten Globule

Question 45

The driving force in the molten globule is

Answer 45

Water exclusion

Question 46

Related to the observation that ‘off-pathway’ folding events are not energetically prohibited. In fact, the energy difference between an on-pathway structural intermediate and an off-pathway structure is only -10 kcal/mol

Answer 46

The need for Chaperones

Question 47

Increase the likelihood of guiding ‘on-pathway’ folding intermediates, ultimately leading to mature and functional proteins

Answer 47

Molecular chaperones

Question 48

Very similar in structure, each containing a barrel with four rings

Answer 48

Proteosome and GroEL chaperone

Question 49

Chaperones use ATP hydrolysis to generate energy and turn it into torque to refold the protein. This requires the hydrolysis of

Answer 49

14 ATP

Question 50

Protect the nascent chain and give guidance during folding to prevent kinetic dead ends

Answer 50

Chaperones

Question 51

Chaperones sitting by the ribosome decide if a protein is folding properly or if it needs to be

Answer 51

Degraded

Question 52

Structurally similar to the chaperone, but its hydrophobic channel is much more narrow, which prevents folded proteins from entering

Answer 52

Proteosome

Question 53

The proteosome is made up of four rings, 2 α and 2 β, and three of these subunits are made up of

Answer 53

Zymogens

Question 54

Consumed in proteosome formation

Answer 54

UMP 1

Question 55

What are the three modules in protein folding?

Answer 55

Hierarchical, Nucleation-condensation, and Hydrophobic collapse

Question 56

Secondary structures form first, and then through intramolecular interactions promote the assembly of the 3-dimensional structure. In the absence of the 3-dimensional interactions, the secondary structure is not stable

Answer 56

Hierarchical module

Question 57

Local sites of structural nucleation results in rapid propagation of the structure motif, which coalesce and stabilize the final native structure

Answer 57

Nucleation-Condensation module

Question 58

The molten globule forms as a result of tertiary hydrophobic interactions that initiate secondary structure maturation and the 3-D structure

Answer 58

Hydrophobic collapse module

Question 59

Cleaves insulin into it's final conformation

Answer 59

Carboxypeptidase e

Question 60

Initially interact with short hydrophobic patches in nascent polypeptide chains, and form a stronger binding with the hydrolysis of ATP.

Answer 60

Cytosolic Hsp70 proteins

Question 61

These cycles of binding and release are coupled to improve folding of the emerging chain, in part by preventing

Answer 61

Non-productive endpoints

Question 62

Do NOT increase the rate of folding reactions, but DO improve the yield of successfully folded products

Answer 62

Chaperones

Question 63

Overcome energetic barriers that slow specific folding steps and can thereby increase folding rates

Answer 63

Protein disulfide isomerase and prolyl isomerase

Question 64

Can transiently bind unfolded segments during the translocation of proteins to the ER and mitochondria, which requires partial unfolding.

Answer 64

Cytosolic Chaperones (Hsp70's)

Question 65

Also present in the lumen of the ER to facilitate refolding and complex assembly

Answer 65

Chaperones

Question 66

Fix improperly formed disulfide bonds and ensure that the correct cysteine residues are paired together

Answer 66

Disulfide isomerases

Question 67

This mutation in the cystic fibrosis transmembrane receptor proteins causes slow folding into the 3D structure. The protein is thus captured by the proteolytic system and degraded.

Answer 67

CFTRΔ508

Question 68

Plays a critical role in recruiting charged tRNA’s to the ribosome, and in ensuring that the correct anticodon::codon pairing ensues. However, when a polypeptide chain fails to fold correctly, it facilitates the degradation of the unfolded chain.

Answer 68

eEF1A

Question 69

In order to form, the proteosome requires

Answer 69

4-5 chaperones

Question 70

Plays an important role in targeting unfolded ER proteins to the cytosolic protein degredation pathway

Answer 70

Endoplasmic Reticulum Associated protein Degredation (ERAD)

Question 71

Promotes the assembly of components of the mitochondrial energy generating pathway -Can be inhibited by geldenamycin

Answer 71

Hsp90

Question 72

The ribosome error rate is

Answer 72

1 out of every 10^4 aminos incorporated

Question 73

A multi-subunit cylindrical particle consisting of four rings that can bind unfolded proteins in large hydrophobic cavities present at both ends of the cylinder -Hydrolyzes 14 ATP per protein

Answer 73

GroEL chaperone

Question 74

The GroEL chaperonin consists of seven identical subunits, which have three distinct domains, termed equatorial, intermediate, and axial. The axial domain forms a large cavity lined with hydrophobic residues that bind

Answer 74

Unfolded Proteins

Question 75

Once the unfolded protein has been captured, the GroEL cavity is covered by the -Prevents premature release of the substrate

Answer 75

GroES complex

Question 76

When GroEL hydrolyzes ATP, it turns, exposing hydrophilic residues in the cavity which cause

Answer 76

Hydrophobic aminos of the protein to be buried in the center (promoting folding)

Question 77

Most neurodegenerative conditions (including Parkinson's, Alzheimer's, and Amyotrophic Lateral Sclerosis) are associated with high levels of

Answer 77

Insoluble proteins (Aggregates)

Question 78

Protein folding also plays a key role in diseases such as mad cow disease and Creutsfeldt-Jakob Disease (CJD), which are both

Answer 78

Prion Diseases

Question 79

Prion diseases can be caused by a mutation in the

Answer 79

PRNP gene

Question 80

A form of transmissible prion disease, which is acquired through ritual cannibalistic activities

Answer 80

Kuru

Question 81

Proteosome substrates can come from co-translational protein misfolding, short-lived regulatory proteins, and

Answer 81

Stress-induced protein damage

Question 82

A large clump of damaged, unfolded proteins all in one area

Answer 82

Aggresome

Question 83

The amyloid diseases share a common feature of accumulating fibrous plaques containing mostly

Answer 83

β-pleated sheet aggregates

Question 84

Protein infectious units that can cause chain reactions of unfolding amongst wild type proteins

Answer 84

Prions

Question 85

Characterized by the accumulation of aberrant Aβ peptide in the plaques

Answer 85

Alzheimer's Disease

Question 86

``` CAG repeats (glutamine) that undergo extensive expansion to cause altered function or aggregation. Ex: Huntington’s Disease, Machado Joseph Disease ```

Answer 86

Trinucleotide expansion diseases