Protein Folding, Misfoldling, and Degradation

Question 1

Planar Peptide Bond

Answer 1

Limits how polypeptide chain can fold; trans or cis configuration

Question 2

Flexibility in a Polypeptide Chain

Answer 2

rotation of the fixed planes of adjacent peptide bonds with respect to one another about two bonds: the Cα -amino nitrogen bond (rotational angle called Φ) and the Cα–carbonyl carbon bond (rotational angle called Ψ); only a limited number of Φ and Ψ angles are possible because, for most Φ and Ψ angles, the backbone or side-chain atoms would come too close to one another, and thus the associated conformation would be highly unstable or even physically impossible to achieve.

Question 3

Peptide-Proline Isomerase

Answer 3

A protein used by cells to catalyze cis/trans isomerizations so that the proline in the folding protein quickly forms the proper isomer

Question 4

Natively Well-Ordered Protein Limits

Answer 4

• Properties of the side chains (size, hydrophobicity, charge, ability to form hydrogen and ionic bonds)
• sequence along the polypeptide backbone

Question 5

Denaturation

Answer 5

Drastic alteration in the conformation of a protein or nucleic acid due to disruption of various non covalent interactions caused by heating or exposure to certain chemicals; usually results in loss of biological function

Question 6

Non-Native Conformations in Proteins

Answer 6

(1) monomeric unfolded or denatured structures
(2) aggregates, which can either be amorphous or have a well-organized structure; can comprise many copies of a single protein (homogeneous aggregates) or contain a mixture of distinct proteins (heterogeneous aggregates)

Question 7

Protein Aggregates

Answer 7

Unfolded and partly folded proteins tend to aggregate into large, often water-insoluble masses, from which it is extremely difficult for a protein to dissociate and then fold into its proper conformation on its own

Question 8

Chaperones

Answer 8

Collective term for two types of proteins – molecular chaperones and chaperoning – that prevent misfolding of a target protein or actively facilitate proper folding of an incompletely folded target protein, respectively; bind to the target polypeptide or sequester it from other partially or fully unfolded proteins, giving nascent protein time to fold properly without colliding into other unfolded proteins

Question 9

Chaperone Binding

Answer 9

Chaperones use a cycle of ATP binding, ATP hydrolysis to ADP, and exchange of a new ATP molecule for the ADP to induce a series of conformational changes that are essential for their function

Question 10

Molecular Chaperones

Answer 10

Bind to a short segment of protein substrate and stabilize unfolded or partly folded proteins, preventing them from aggregating and being degraded; begin binding to a new protein even before its synthesis is complete

Question 11

Chaperonins

Answer 11

Form folding chambers into which all or part of an unfolded protein can be sequestered, giving it time and an appropriate environment to fold properly

Question 12

Hsp70

Answer 12

Heat shock proteins are the major molecular chaperones in all organisms that use an ATP-dependent cycle to facilitate proper folding of their substrates.

Question 13

Hsp70 Cycle

Answer 13

1. Substrate binding to the “open” ATP-bound Hsp70
2. Substrate binding induces ATP hydrolysis to ADP that leads to a “closed” ADP-bound Hsp70 conformation that binds substrate much more tightly
3. Inhibition of substrate misfilings or aggregation while bound tightly to the closed Hsp70. In a sense, Hsp70 acts by inhibiting inappropriate protein folding
4. Exchange of ATP for ADP on the Hsp70 with its conversion to the “open” conformation
5. Release of the substrate protein and its subsequent folding

Question 14

Hsp90

Answer 14

Recognize partially folded substrate proteins (clients); helps cells fold partially folded clients, cope with denatured proteins generated by stress, and ensure that some of their clients can be converted from an inactive to an active state or otherwise held in a functional conformation

Question 15

Hsp90 Cycle

Answer 15

Partially folded clients bind to the substrate-binding domains when the chaperone is in the “open” conformation, that ATP binding leads to interaction of the ATP-binding domains and formation of a “closed” conformation, and that hydrolysis of ATP plays an important role in the activation of some client proteins and their subsequent release from the Hsp90

Question 16

Group I Chaperonins

Answer 16

Composed of two rings, each having seven subunits that interact with a co-chaperone lid that also has seven subunits; each ring is a folding chamber into which an unfolded protein enters

Question 17

Group II Chaperonins

Answer 17

Can have eight to nine homomeric or heteromeric subunits in each ring, and the lid function is incorporated into this subunits themselves – no separate lid protein is needed; ATP hydrolysis triggers the closing of the lid

Question 18

Amyloid

Answer 18

Protein aggregate formed from elevated concentrations or changes in environmental conditions; resistant to enzymatic degradation

Question 19

Three Ways to Regulate Protein Activity

Answer 19

1. Cells can increase or decrease the steady-state level of the protein by altering its rate of synthesis, its rate of degradation, or both
2. Cells can change the intrinsic activity, as distinct from the amount, of the protein
3. Change in location or the concentration within the cell of the protein itself, of the target of the protein’s activity (e.g. an enzyme’s substrate), or of some other molecule required for the protein’s activity (e.g. an enzyme’s cofactor)

Question 20

Rate of Synthesis of a Protein

Answer 20

Determined by the rate at which DNA encoding the protein is converted to mRNA (transcription), the steady-state amount of the active mRNA in the cell, and the rate at which the mRNA is converted into newly synthesized protein (translation)

Question 21

Protein Degradation

Answer 21

Removes proteins that are potentially toxic, improperly folded or assembled, or damaged – including the products of mutated genes and proteins damaged by chemically active cell metabolites or stress such as heat shock

Question 22

Proteostasis

Answer 22

The process of maintaining proteins and their activities at appropriate levels, and for making rapid adjustments in these levels in response to changing conditions

Question 23

Lysosomal Degradation

Answer 23

Pathway with lysosomes for degrading aged or defective organelles of the cell and extracellular proteins taken up by the cell

Question 24

Proteasome

Answer 24

Large multifunctional protease complex in the cytosol that degrades intracellular proteins marked for destruction by attachment of multiple ubiquitin molecules

Question 25

Proteasomal Degradation

Answer 25

1. Protein is tagged to target it for proteasomal degradation
2. Proteasome binds to the targeted protein via the tag and unfolds the protein as it is transferred into an internal chamber
3. Protein-cutting subunits of the proteasome within the chamber degrade the target protein into small peptides, which are releases into the cytosol for further processing

Question 26

Ubiquitinylation Process

Answer 26

1. Activation of ubiquitin-activating enzyme (E1) by the addition of a ubiquitin molecule, a reaction that requires ATP
2. Transfer of this ubiquitin molecule to a cysteine residue in a ubiquitin-conjugating enzyme (E2)
3. Formation of a covalent bond between the carboxyl group of theC-terminal glycine 76 of the ubiquitin bond to E2 and the amino group of the side chain of a lysine residue in the target protein, a reaction catalyzed by a ubiquitin-protein ligase (E3)

Question 27

E3 Ligase

Answer 27

Target specific proteins for proteasomal degradation

Question 28

Allostery

Answer 28

Change in the tertiary and/or quaternary structure of a protein induced by binding of a small molecule to a specific regulatory site, causing a change in the protein’s activity

Question 29

Cooperativity

Answer 29

The influence that the binding of a ligand at one site has on the binding of another molecule of the same type of ligand at another site

Question 30

Post-Translational Modifications (PTMs)

Answer 30

The covalent and generally enzymatic modification of proteins following protein biosynthesis

Question 31

Phosphorylation

Answer 31

The covalent addition of a phosphate group to a molecule such as a sugar or a protein; the hydrolysis of ATP often accompanies phosphorylation, providing energy to drive the reaction and the phosphate group that is covalently added to the target molecule

Question 32

Phosphatase

Answer 32

An enzyme that removes a phosphate group from a substrate by hydrolysis. Phosphoprotein phosphates act with protein kinases to control the activity of many cellular proteins

Question 32

Kinase

Answer 32

An enzyme that transfers the terminal (Y) phosphate group from ATP to a substrate. Protein kinases, which phosphorylate specific serine, threonine, or tyrosine residues, play a critical role in regulating the activity of many cellular proteins