Term
| What separates the contents of an organelle from the cytosol? |
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Definition
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Term
| What's the point of having organelles? |
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Definition
| Confine different metabolic processes and proteins required to perform them within different organelles. Provides sequestered environments. |
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Term
| What is the function of the cytosol? What happens there? |
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Definition
| Contains many metabolic pathways; protein synthesis and degradation |
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Term
| What is the function of the nucleus? What happens there? |
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Definition
| Contains genome; DNA and RNA synthesis; RNA processing |
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Term
| What is the function of the Endoplasmic Reticulum? What happens there? |
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Definition
| Synthesis of proteins and lipids |
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Term
| What is the function of the Golgi apparatus? What happens there? |
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Definition
| Modification; sorting and packaging of proteins and lipids |
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Term
| What is the function of the lysosomes? What happens there? |
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Definition
| Intracellular degradation |
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Term
| What is the function of the mitochondrion? What happens there? |
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Definition
| ATP synthesis by oxidative phosphorylation |
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Term
| What is the function of the peroxisomes? What happens there? |
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Definition
| Oxidation of toxic materials |
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Term
| What is the classical principle in protein folding? |
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Definition
| all the information for a protein to adopt the correct 3-dimensional structure is provided by amino acid sequence |
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Term
| What about the amino acid sequence causes protein folding (in the classical view)? |
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Definition
| The hydrophobic residues collapse to hide from water. |
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Term
| What type of structure is protein folding? (ie 1/1, 2/2, 3/3, 4/4) |
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Definition
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Term
| Is the classical principle in protein folding what happens in real life? Why/why not? |
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Definition
| No, cellular conditions are not optimal for spontaneous protein folding, and often results in protein aggregation. Chaperone proteins suppress aggregation and facilitate folding. |
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Term
| What are molecular chaperones? |
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Definition
| They are proteins which facilitate folding. |
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Term
| Do chaperone proteins end up being a part of the final protein complex? |
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Definition
| No, once folding occurs they go away. |
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Term
| What happens when a polypeptide doesn't get folded right? |
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Definition
| It gets aggregated and then degraded. |
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Term
| Can chaperones bind partially-folded polypeptides? |
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Definition
| Yes, they bind unfolded and/or partially folded peptides and prevent aggregation. |
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Term
| What are heat shock proteins? |
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Definition
| Heat shock proteins are chaperones. They facilitate the folding of proteins that are partially denatured by heat. |
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Term
| In what type of cell conditions are heat shock proteins expressed? |
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Definition
| stressed conditions (eg high temp) |
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Term
| Do heat shock proteins bind to hydrophilic or hydrophobic residues? |
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Definition
| They bind to hydrophobic residues. |
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Term
| What do HSPs use for energy? |
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Definition
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Term
| When do HSPs work? Pre/during/post translation? |
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Definition
| They work during synthesis |
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Term
| What do HSPs do? (hint: 2 possibilities) |
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Definition
| They facilitate folding during translation under stressed conditions. OR they bring the polypeptide to a chaperonin complex to facilitate folding. |
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Term
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Definition
| It is a multiprotein subunit complex. |
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Term
| How is chaperonin structured? |
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Definition
| The subunits are arranged in two stacked rings to form a double chambered structure. |
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Term
| What's the point of the chamber in chaperonins? |
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Definition
| The chamber is where the polypeptide goes. There it is shielded from the cytoplasm, so can fold correctly without forming aggregates with other proteins. |
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Term
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Definition
| It is a 76 amino acid polypeptide used as a marker to target proteins for degradation. |
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Term
| Where does ubiquitin get attached? |
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Definition
| It attaches to the side chain of lysines in the target protein. |
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Term
| What is a polyubiquitin chain? |
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Definition
| It is when lots of ubiquitin get attached to form a polyubiquitin chain. |
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Term
| Go through the steps of Ubiquitination...lol |
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Definition
| 1. Ubiquitin is attached to a 'Ubiquitin activating enzyme' called E1. 2. Activated ubiquitin is transferred to a 'Ubiquitin conjugating enzyme' called E2. 3. E2 conjugated ubiquitin is transferred to the target protein with the help of 'Ubiquitin ligase' also called E3. 4. Poly ubiquinated proteins are delivered to a proteasome for degradation. |
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Term
| Why is Ubiquitin called that? |
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Definition
| Because it is ubiquitous within the cell. |
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Term
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Definition
| They degrade/break down proteins |
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Term
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Definition
| It is a protein complex containing proteases and peptidases. |
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Term
| What is the structure of a proteasome? |
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Definition
| It contains 4 stacked rings and a regulatory particle that serves as a lid where polyubiquitin binds. |
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Term
| The core region of the proteasome contains what type of enzyme activity? |
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Definition
| trypsin-like, chymotrypsin-like, and peptide glutamylpeptido hydrolase activity. |
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Term
| What is the sole purpose of proteasomes? |
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Definition
| To break-down misfolded proteins. |
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Term
| What activates ubiquitin? |
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Definition
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Term
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Definition
| E1 transfers ubiquitin to E2, and E2 conjugates ubiquitin (meaning it attaches to it). |
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Term
| What transfers ubiquitin to the target protein? |
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Definition
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Term
| How many ubiquitins does a protein need to go to the proteasome? |
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Definition
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Term
| What are two diseases related to failure of protein folding? |
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Definition
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Term
| What are 2 places where proteins are made? |
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Definition
| free ribosomes in the cytoplasm, ribosomes on the rough ER |
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Term
| What are the possible destinations of proteins made on the free ribosomes? |
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Definition
| cytoplasm, peroxisome, mitochondria, nucleus |
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Term
| What are the possible destinations of proteins made on the rough ER? |
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Definition
| can end up in ER, golgi, lysosome, cell membrane as transmembrane proteins, cell membrane in extracellular matrix (outer leaflet), peroxisomal membranes, or excreted into blood and outside of the cell. These locations are all considered EXTRACELLULAR. |
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Term
| What about the cytosol makes it unconducive for protein folding? |
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Definition
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Term
| In layman's terms, what do chaperones do? |
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Definition
| They prevent the nascent polypeptides from getting too close to other proteins, and they get them where they need to go. |
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Term
| At what step is ATP used in ubiquitination? |
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Definition
| Binding Ubiquitin to E1. ATP is also used by the proteasome to break down polypeptides. |
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Term
| What happens when the cell is under stress with regard to chaperones? |
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Definition
| The cell needs more chaperones, so reserve chaperones are released from the ER. Release of reserve proteins from the ER signals the cell and transcription factors then upregulate chaperone expression. |
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Term
| What are two enzymes involved with protein folding? |
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Definition
| peptidyl prolyl isomerase (accelerates protein folding), protein disulphide isomerase (helps proteins with their cysteine bonds, found in the ER) |
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Term
| How is protein folding a part of quality control? |
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Definition
| Misfolded proteins don't work well, or at all, and could even cause damage. So, quality control has to do with getting them either in the right conformation, or degraded. |
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Term
| What does protein aggregation do to cells? |
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Definition
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Term
| What type of secondary structure allows proteins to function properly in a water-filled environment? |
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Definition
| Hydrophobic regions inside, hydrophillic on outside |
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Term
| If proteins can fold normally on their own, why do you need chaperones? |
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Definition
| It would take too long for proteins to fold on their own, also there would be too much misfolding. |
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Term
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Definition
| Well, HSP 70 binds a protein along with the HSP 40 helper protein. HSP 70 then hydrolyzes a molecule of ATP-->ADP, causing it to have a conformational change and locks it tightly around the protein. After HSP 40 leaves, ATP replaces the ADP on HSP 70, causing it to dissociate as well. |
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Term
| What class of HSPs come in if HSP 70 fails to get proper folding? |
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Definition
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Term
| When protein aggregation occurs, what property clumps them together? |
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Definition
| The hydrophobic regions all sorta congregate, and you then precipitate clumps of aggregated proteins out of solution. |
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Term
| What are the three parts of HSP 70? |
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Definition
| N terminus that binds ATP, middle part that binds 7-9 hydrophobic AA's, C terminal lid that clamps the protein |
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Term
| After HSP70 is done, what helps it to get rid of ADP and get ATP back so it can loosen up and release the protein? |
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Definition
| HSPBp = nucleotide exchange factor |
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Term
| What type of molecule is HSP 60? |
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Definition
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Term
| How does HSP60 capture proteins? |
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Definition
| It has a hydrophobic region along the HSP60 barrel's rim. |
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Term
| After a protein is captured by HSP60, what happens? |
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Definition
| ATP and the GroES cap binds the HSP60 chaperonin. This causes the barrel gets stretched out, stretching out the protein. Then the protein has a chance to refold. It gets ejected after about 15 seconds when ATP is hydrolyzed. |
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Term
| Where is protein disulfide bonding not a problem? |
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Definition
| So in the cytoplasm, have a reducing environment. SO, the proteins get their disulfide 2/2 structure fine. IN the ER, it is an oxidizing environment, so things get messed up and need peptidyl disulfide isomerase (PDI). Basically, in the cytoplasm, a hydrogen will come and bind the S, but in the ER the S could bind with another protein's S. |
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Term
| What helps the protein fix its cis-trans isomerization? |
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Definition
| Peptidyl Prolyl Isomerase (PPI) (only those involving proline tho) |
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Term
| What tendency do proteins in the ER have that peptidyl disulfide isomerase (PDI) can prevent? |
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Definition
| Proteins will get disulfide cysteine bonds with each other, or with the wrong cysteine residue sometimes. PDI will bond the cysteine residues to free them and then the proper disulfide binding will occur. |
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