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Biochemistry-Jourdan > Protein Folding II > Flashcards

Protein Folding II Flashcards

1
Q

What protein turnover?

A

Balance between protein production and protein degration

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2
Q

What are four things that contribute to protein stability?

A

Hydrophobic effect, Disulfide bonds, oligomers, and cosmotrophs

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3
Q

How do disulfide bonds stabilize a protein?

A

Oxidation forms disulfide bonds and extracellular fluid is oxidative. Thus disulfide bonds outside the cell stabilized proteins.

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4
Q

How does the hydrophobic effect stabilize a cell?

A

Keeps the fat on the inside of the protein

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5
Q

Explain UPS/UPR

A

Unfolded protein stress/response. When a protein unfolds and remains unfolded the cell is going to respond to that stress. Highly involves the ER

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6
Q

If a cell detects UPS/UPR what are some responses?

A

halting protein translation, degrading misfolded proteins and activating the signaling pathways that lead to increasing the production of molecular chaperones involved in protein folding. If these objectives are not achieved within a certain time lapse or the disruption is prolonged, the UPR aims towards apoptosis.

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7
Q

What are cosmotrophs?

A

Small molecules that contribute to stability of proteins

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8
Q

What is a C3 symmetry?

A

Three fold symmetry. Able to rotate it 1/3 around the circle and its the same molecule

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9
Q

What is D3 symmetry?

A

3 Subunits stack on another 3 subunit. On a right angle it can flip and then rotate to be the same molecule. Second rotation is 90 degrees from the first one. Dihedral

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10
Q

What is an example of screw symmetry?

A

Actin filaments and micro tubules. Globular proteins wrapped around each other in a cyclical fashion. Turn and see the same thing

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11
Q

What three conditions cause protein denaturation?

A

Heat, pH extremes, and agitation

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12
Q

What three chemicals contribute to protein denaturation?

A

Detergents, chotropic agents and organic solvents

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13
Q

What happens to proteins in eggs when heat is added?

A

the clear whites turn white because the hydrophobic residues are now exposed and then pop back together and aggregate together

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14
Q

What cooking technique is an example of pH denaturing proteins?

A

Civiche. Acidity of lemon can cause the shrimp to turn white

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15
Q

How can agitation cause protein denaturation?

A

In a concussion, it may create an agitation that may contribute to some denaturations in the brain. Or if an egg white is beat it turns white

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16
Q

How do detergents denature proteins?

A

Fat and hydrophilic portion in detergents disrupt the hydrophobic core

17
Q

What chaotropic agents contribute to protein denaturation?

A

Urea and guanididium chloride

18
Q

What organic solvent can denature proteins?

A

Alcohols

19
Q

What are the methods of analysis?

A

Turbidity, circular dichroism, UV absorption, Fluroescence, Biological activity

20
Q

What is turbidity?

A

Protein goes in a covet and into a spectrometer to measure wavelength. Protein gets cloudy

21
Q

What is circular dichroism?

A

Looks at secondary structure and determins % of alpha helix and beta strands

22
Q

What proteins are used with UV absorption and fluorescence analysis?

A

Connected to aromatic proteins.

23
Q

How is biological activity used to analyze?

A

Fully folded will be functional and unfolded will not be.

24
Q

What does Urea and beta-mercapteoethanol do to ribonucleases?

A

Ribonuclease is an extracellular digestive enzyme so it has disulfide bonds and Urea and beta - mercapteoethanol reduce ribonucleases.

25
Q

What is the difference between quanidinium and guanidine?

A

Quanidinium is the protenated name ad Quanidine is deprotenated

26
Q

What is PDI

A

Protein disulfide isomerases that recognize messed up disulfide linkages. Breaks and reforms linkages

27
Q

What is PPI?

A

Protein cis-trans prolyl isomerases - Recognizes and fixes the orientation of the peptide bond if proline creates a kink and causes a trans to turn to cis or vice versa

28
Q

What are HSP 70 (HSP 40)

A

Chaperones that are ATP-driven and reverses msfolds; newly synthesized proteins;unfold/refold of trafficked proteins

29
Q

What is the HSP 90 chaperone used for?

A

Signal transduction proteins - they can be intrinsically unstructure and their chances of falling out of their ensemble of conformations is possible. HSP 90 refolds them

30
Q

What are nucleoplasms?

A

Chaperones involved in nucleosome formation and ribosome biogenesis as well.

31
Q

What are small - HSP?

A

Chaperones that preven aggregation. They work in conjunction with HSP 70 and 40.

32
Q

What are chaperonins?

A

Rings or basket like chaperones and major sub straits are actin monomers and tubulan monomers

33
Q

What is GroEL/ES?

A

GroELBelongs to the chaperonin family of molecular chaperones, and is found in a large number of bacteria. It is required for the proper folding of many proteins.

To function properly, GroEL requires the lid-like cochaperonin protein complex GroES. Has a C7 symmetry with the cap or a D7 symmetry without the cap

34
Q

What group found in the mitochondria of eukaryotes is similar to GroEL/ES

A

HSP60/HSP 10 In eukaryotes the proteins Hsp60 and Hsp10 are structurally and functionally nearly identical to GroEl and GroES, respectively

35
Q

In chaperonins what are the sections of the subunit

A

Apical, intermediate and equatorial. Equatorial domain determines the floor of this domain

36
Q

What is the basic mechanism of chaperonins

A

It is like a two stroke engine. One ring is working and the other is not. In the first ring, the misfolded protein binds to the apical orface of the basket. The cap comes on and may possibly (theory) stretch the basket to allow the protein to drop in the basket to allow the protein to explore multiple conformations to reach its real conformation. Energy released as heat to unfold the protein a little so if it fell into a misfold that was unstable it can unfold in a protected environment then refold.

37
Q

What are the two models of chaperonins?

A

Anifinsen cage: Allow the protein to passively find its proper form
Iterative (active or annealing): inner portion of basket interacts with the misfolding until it gets to proper form

Biochemistry-Jourdan (8 decks)

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