Term
| How do nascent proteins reach their final conformation? |
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Definition
- bring hydrophobic residues inside when a protein folds (Energetically favorable)
- form alpha helices and beta sheets.
- combine with cofactors.
- become covalently modified at specific sites.
- form quaternary structures with subunits.
A combination of these arrangements determines the final folding pattern of the polypeptide chain.
Some proteins fold into subdomains as they are extruded from the ribosome |
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Term
| Some proteins need help to fold properly |
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Definition
Chaperones: A set of proteins that help cellular proteins fold correctly or refold correctly
Hsp: (Special class of chaperones) heat shock proteins. Chaperones are heat shock proteins, i.e., made in large quantities at high temperature. Proteins are more likely to “denature” at high temperatures and require refolding.
These proteins have two properties: 1) they bind to hydrophobic patches and 2) require ATP hydrolysis |
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Term
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Definition
| A set of proteins that help cellular proteins fold correctly or refold correctly |
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Term
| Hsp (Heat Shock Proteins) |
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Definition
| heat shock proteins. Chaperones are heat shock proteins, i.e., made in large quantities at high temperature. Proteins are more likely to “denature” at high temperatures and require refolding. |
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Term
| Two types of heat shock proteins |
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Definition
hsp70
bind to exposed hydrophobic amino acid sequences as polypeptides exit the ribosome
- appear to prevent hydrophobic regions from aggregating in a nonspecific manner
hsp60
Acts after a protein has been synthesized
forms basket with hydrophobic sides
- confinement gives protein time to refold without interference of other cellular proteins |
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Term
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Definition
bind to exposed hydrophobic amino acid sequences as polypeptides exit the ribosome
- appear to prevent hydrophobic regions from aggregating in a nonspecific manner |
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Term
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Definition
Acts after a protein has been synthesized
forms basket with hydrophobic sides
- confinement gives protein time to refold without interference of other cellular proteins |
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Term
| Molecular Chaperones help guide the folding of most proteins |
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Definition
1) On-pathway folding
2) Off-pathway folding - can be brought back by molecular chaperone catalysis
3) Irretrievable accidents - degraded |
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Term
| What if a protein never folds correctly or denatures inside the cell? |
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Definition
can fold correctly by itself
can fold correctly with chaperones
incompletely folds - degraded by proteasome
if not degraded, can become protein aggregate |
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Term
| The proteasome consists of a core capped by two regulatory particles |
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Definition
19S regulatory particle
20S core particle
19S regulatory particle
hydrolyze peptide bonds
Some of the subunits of the core are proteases that hydrolyze peptide bonds. |
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Term
| Some proteases have specificity. |
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Definition
Digestive proteases:
trypsin — carboxyl side of lysine and arginine (positively-charged residues), except when followed by proline)
- chymotrypsin — carboxyl side of tyrosine, tryptophan and phenylalanine (all contain aromatic rings) |
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Term
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Definition
| carboxyl side of lysine and arginine (positively-charged residues), except when followed by proline) |
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Term
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Definition
| carboxyl side of tyrosine, tryptophan and phenylalanine (all contain aromatic rings) |
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Term
| Three subunits of the beta rings are proteases. |
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Definition
1. trypsin-like activity
2. chymotrypsin-like activity
3. post-glutamyl-peptide hydrolytic activity (cleaves after acidic or branched-chain amino acid)
Stack of four heptameric rings
core hydrolyzes peptide bonds - all of them but with different subunits |
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Term
| The regulatory subunits have many functions. |
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Definition
functions:
1. substrate recognition
2. ubiquitin releasing
3. substrate unfolding |
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Term
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Definition
polyubiquitin is what is recognised by regulatory subunits
Ubiquitin is a protein of 76 amino acids, highly conserved among eurkaryotes. Discovered in early 1980s and the discovery won Nobel Prize in 2004.
The recognition signal is polyubiquitin |
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Term
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Definition
hexameric unfoldase in the base (recognition tag is polyubiquitin)
The unfoldase subunits are AAA proteins that hydrolyze ATP as they work. They are related to hexameric DNA helicases.
The unfoldase is normally processive, working residue by residue to unfold the protein.
(AAA ATPase Associated with diverse cellular Activities) |
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Term
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Definition
| ATPase Associated with diverse cellular Activities |
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Term
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Definition
is a protein of 76 amino acids, highly conserved among eurkaryotes. Discovered in early 1980s and the discovery won Nobel Prize in 2004. NOT IN BACTERIA
Glycine is 75 and 76 AA of ubiquitin - carboxyl group of ubiquitin bonds to R group of Lysine 48 by isopeptide bond. Then, lysine from ubiquitin and glycine from next ubiquitin creates peptide bond.
Ubiquitin is covalently attached to target proteins
The isopeptide bond is made from the C-terminal glycine of ubiquitin to the epsilon amino of lysine resides on target proteins.
Polyubiquitin is made by adding ubiquitin to ubiquitin.
Polyubiquitin chains are made between the C-terminal glycine of one ubiquitin to the amino of lysine 48 on a second ubiquitin. |
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Term
| The regulatory complex contains one or more enzymes, dubbed |
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Definition
| DUBs (deubiquitinating enzyme), that hydrolyze the isopeptide bond to recycle ubiquitin monomers |
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Term
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Definition
| deubiquitinating enzyme, that hydrolyze the isopeptide bond to recycle ubiquitin monomers |
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Term
| Ubiquitination can be detected by Western blotting |
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Definition
each ubiquitination is addition of 8kb Daltons
see a ladder going up from the original protein |
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Term
| The isopeptide bond is made in a series of three steps |
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Definition
1) E1 — ubiquitin activating enzyme (high-energy thioester linkage to a cysteine side chain on E1) few in a cell (eu-only 2, pro only 1)
2) E2 — ubiquitin conjugating protein (activated ubiquitin is transferred to cysteine on E2)
3) E3 — ubiquitin ligase (E2 and E3 work together - most important - transfers it to the protein) |
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Term
| E3, ubiquitin ligase, is responsible for recognizing the target protein |
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Definition
Ubiquitin ligase transfers ubiquitin to the target protein and also builds polyubiquitin chains.
**specificity by E3, and E2 for transfer |
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Term
| The number of genes encoding the ubiquitin system reflects its specificity |
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Definition
E1 - activating enzyme - 1 or 2 only
E2 - conjugating enzyme - dozens
E3 - ubiquitin ligase - 100's |
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Term
| The number of genes encoding the ubiquitin system reflects its specificity |
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Definition
RING domain
HECT domain
Note that RING E3s transfer ubiquitin to the target directly from the E2, while HECT E3s themselves are ubiquitinylated before transfer. |
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Term
| Degradation of Cdc6 to activate DNA replication |
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Definition
| An example of degradation phophorylated and then ubiquitinated |
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Term
| The ubiquitin conjugation system is used for more purposes than protein degradation |
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Definition
1. Some target proteins are monoubiquitylated (not polyubiquitylated). This may serve to target proteins to cellular locations.
2. Cells possess other ubiquitin-like proteins that are usually added singly to targets. SUMO —small ubiquitin-like modifier is one such paralog that aids in controlling the activity of target proteins.
3. Polyubiquitin chains can form between Lys6, Lys11, Lys27, Lys29, Lys33 and Lys63, not just Lys48. The meaning of these alternative linkages is not currently known. |
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Term
Some target proteins are monoubiquitylated (not polyubiquitylated). This may serve to target proteins to cellular locations.
Cells possess other ubiquitin-like proteins that are usually added singly to targets. SUMO —small ubiquitin-like modifier is one such paralog that aids in controlling the activity of target proteins.
3. Polyubiquitin chains can form between Lys6, Lys11, Lys27, Lys29, Lys33 and Lys63, not just Lys48. The meaning of these alternative linkages is not currently known. |
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Definition
monoubiquitylation - histone regulation
multi-ubiquitylation - endocytosis
polyubiquitylation - proteasomal degradation or DNA repair |
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Term
| A number of human diseases are caused by proteins that misfold and wreck havoc before they can be degraded. |
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Definition
Stack of beta sheets.
Resistant to proteolysis
a rare conformation change can cause infectious seeding of amyloid fiber formation
heterodimer, homodimer, amyloid (infectious) - the stacking is resistant to degradation |
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Term
| A combination of covalent and non-covalent interactions determine |
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Definition
| the final folding pattern of a protein. |
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Term
| Two types of chaperone proteins, called |
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Definition
| heat shock proteins (hsp) help proteins fold. |
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Term
| The hsp70 proteins bind to |
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Definition
| hydrophobic patches to help them gain the interior of soluble globular proteins. |
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Term
| The hsp60 proteins are a hydrophobic chamber that |
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Definition
| help misfolded proteins regain their proper conformation. |
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Term
| Controlled protein degradation is an important mechanism of |
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Definition
| regulating gene expression. |
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Term
| Proteins are degraded by the |
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Definition
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Term
| The proteasome is composed of |
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Definition
| a 20S cylindrical core containing proteases and two 19S regulatory particles. |
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Term
| The 20S core is composed of |
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Definition
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Term
| The two inner rings contain proteases with specificities of |
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Definition
| trypsin (basic amino acids), chymotyrpsin (aromatic amino acids) and a post-glutamic acid protease. |
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Term
| Proteins destined for the proteasome must be |
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Definition
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Term
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Definition
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Term
| Ubiquitin is attached to the amino group of |
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Definition
| lysine residues on target proteins through an isopeptide bond with its C-terminal glycine residue |
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Term
| Chains of ubiquitin are made by addition to |
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Definition
| Chains of ubiquitin are made by addition to |
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Term
| Polyubiquitinylation occurs in three steps |
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Definition
| 1) The ubiquitin activating enzyme, E1, attaches ubiquitin to itself as a thiol ester with the C-terminal glycine. 2) The ubiquiting conjugating protein, E2, effects the transfer of ubiquitin to itself, again as a sulfur ester. 3) Ubiquitin ligase, E3, transfers the ubiquitin to the target protein. |
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Term
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Definition
| E3s because these enzymes must possess specificity in recognizing the many target proteins in the cell. |
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Term
| Two large gene families of E3s are the |
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Definition
| RING domain and the HECT domain E3s. |
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Term
| Unfolded proteins that escape degradation form |
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Definition
| protein aggregates. These aggregates form amyloid plaques which are prominent in Huntington’s disease and Alzheimer’s. |
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