Term
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Definition
| mitochondria probably evolved from bacteria engulfed by large, ancient eukaryotic cells. A predatory cell took in a prokaryotic cell, but it had a mutation in the mechanism for breaking the prokaryotic cell down for food. The prokaryote was able to do aerobic respiration, and continued to pump out ATP while inside the eukaryotic cell, and allowed the mutant eukaryotic cell to outperform its peers. |
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Term
| Adenosine Monophosphate (AMP) |
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Definition
| There is more of this protein in energy depleted cells. It binds to AMP Kinase, as does ATP. ATP turns it off. |
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Term
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Definition
| Proteins that catalyze the attachment of phosphates to other molecules. They bind to a target substrate (one per kinase) and to ATP. Proteins with ATP binding domain are likely to be kinases. Serine, Tyrosine, and Threonine are the target amino acids. Every protein with one of these amino acids has the potential to be bound to consensus phosphorylation sites (which are certain sequences with T, Y, and S that tend to be bound by kinases). Kinases that attach phosphates to Tyrosine side chains are Protein Tyrosine Kinases. Kinases that attach phosphates to Serine or Threonine side chains are Protein Serine/Threonine Kinases. These kinases can bind to Serines on some proteins and then Threonines on others. Kinases attach the phosphate to the target protein covalently. |
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Term
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Definition
| proteins that catalyze the removal of phosphates from other molecules. Protein Tyrosine Phosphatases remove phosphates from Tyrosines. Phosphatases that remove phosphates from Serines or Threonines are Protein Serine/Threonine Phosphatases. They will find a certain phosphorylated Serine or Tyrosine and clip the phosphate off at the right time. A Kinase might come by a minute later to turn the protein back on again. |
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Term
| Phosphorylation and Dephosphorylation |
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Definition
| Through phosphorylation or dephosphorylation, they turn proteins on or off, and can trigger their degradation. They can also trigger protein interactions or disrupt them. Phosphorylation or dephosphorylation can also change the subcellular location of the target protein. For every kinase in a cell, there should be a counter-acting phosphatase. All of these actions that can be triggered by kinases and phosphatases allow them to regulate the cell cycle, metabolism, growth pathways, and more. These proteins are studied in cancer a lot. |
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Term
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Definition
| Some individual proteins are regulated by multiple kinases and phosphatases. The phosphorylation by the first protein on the target protein activates the catalytic function of the target protein. Phosphorylation of a different amino acid on the target protein by a second kinase causes the target protein to change its shape so that it can now interact with a different protein. |
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Term
| Phosphorylation amino acid substitutions |
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Definition
| You can also mess with the amino acids to see which one was bound to by the kinase. You can mutate the codons for the amino acids of interest (like changing a Y to an F, they both have phenyl groups, but Y has a hydroxyl group and can be phosphorylated). You can change any amino acid to any other amino acid if you have the DNA isolated. Changing an S to an N gives you an amino acid that kind of resembles the phosphorylated state of S. This allows you to mimic the phosphorylated state, and see what happens if the protein is ‘phosphorylated’ permanently. You could change the S to an aspartic acid to have an amino acid with a negative charge. |
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Term
| Radioactive phosphorylation |
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Definition
You can put the cell with the protein of interest in a cell lysate and put radioactive ATP in (where the third Phosphate is radioactive). If the protein is phosphorylated, it will end up radioactive.
You could make a mutant form of the protein without the S of interest, make it radioactive, and put it in a lysate. If it doesn’t get phosphorylated, this means that the S that you removed was the one that gets phosphorylated, and then you freak out. You can do this with any amino acid of interest, until you find one that is right. |
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Term
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Definition
| molecules can be trafficked from one area of the cell to another in continuity (if water molecules can flow between two areas, they’re in continuity), without crossing or going through any barriers. This happens pretty much only between the nucleus and the cytoplasm, since the nuclear pores are water-filled channels that water and ions can flow through. Big molecules can’t just go through, and neither can RNA. They must be recognized by a pore complex to go through. nucleus and the cytosol |
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Term
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Definition
| molecule travels from one side of an intact membrane to the other side. Proteins are trafficked through membrane bilayers through embedded proteins. This way, ions and water molecules don’t get to go through, and the membrane is kept intact. Transporter proteins route proteins through the membrane, as in the ER when proteins are inserted as they are synthesized. between the cytosol and then peroxisomes, plastids, mitochondria, ER |
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Term
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Definition
| happens when a protein in a membrane-bound organelle needs to travel to another organelle, so it buds a pod (vesicle) off of the organelle and travels to a new one. Proteins travel from the ER to the Golgi in this manner.happens between the ER and the Golgi, the Golgi and the endosomes, secretory vesicles, cell surface, and lysosomes |
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Term
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Definition
| proteins that make DNA from RNA. The proteins are found in viruses, which put their own RNA into a cell to use as a template to make DNA to incorporate into the host cell’s chromosomes. |
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Term
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Definition
| Different cell types have the same genes (a few exceptions). The translation and transcription of these genes can be regulated differently in different cell types via siRNA and snRNA. This allows the cell to turn genes on or off or to amplify or reduce their expression. This is what makes different cell types differ. |
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Term
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Definition
| (complimentary DNA). If you isolate an mRNA strand and put it in with a Reverse Transcriptase, it will make a single-stranded cDNA. If you put DNA polymerase in with the cDNA, it will render it into a double-stranded cDNA. This cDNA will lack introns, unlike the gene the template mRNA would have come from. To get cDNA, you would look in the cytoplasm for the mRNA from the gene of interest, since the mRNA has been fully processed and had all the introns taken out. If you transcribe the cDNA, you’ll get the original mRNA again. You can predict the amino acid sequence of the encoded protein easily from a cDNA molecule. cDNA is basically a gene with no introns, making it very useful. |
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Term
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Definition
| made by taking a bunch of homogenous cells, splitting them open, and extracting the mRNA. The cDNA will only represent the expressed genes, so you get a library of what genes are expressed in a certain cell at a certain moment. The cDNAs you get when using Reverse Transcriptase are more varied than the original assortment of mRNA molecules, because some cDNA molecules are full versions of mRNA, and some are partial. The library of cDNA molecules encased in plasmids represents all the genes that were expressed in the cell at the time of lysing. |
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Term
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Definition
| isolate the cytoplasm from a colony of homogenous cells. You want only the mRNA in the cytoplasm, not any of the tRNA or rRNA molecules. To go after the mRNA only, you can target the poly-A tail on the 3’ end or the 7-methylguanosine cap on the 5’ end. To target the poly-A tail, you can put in tiny beads covered in singe strands of poly-T DNA. These beads are used as a fishing lure. After incubating the cytoplasm with the beads, the Ts and As will base pair up, and the mRNA molecules will be attached to the beads. If you centrifuge the cytoplasm and wash it down, you’ll be left with the beads on the bottom, and a bunch of different mRNA molecules. You won’t get any silent genes in this mix. The more abundantly a gene is transcribed, the more mRNA made from it there will be. Purified Reverse Transcriptases will produce cDNA using all the mRNA molecules as templates. You use a well-characterized plasmid vector to capture the cDNA molecules in, by cutting the plasmid open at a specific place and putting the cDNA in. This means that all the plasmids are the same, but they each contain a different stretch of cDNA (like books with the same jacket but different contents). |
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Term
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Definition
| proteins that form a mesh in the inner nuclear envelope, and keep the nuclear envelope strong, to secure the nucleus |
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Term
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Definition
| All the proteins that make up a nuclear pore.There are at least 50 different kinds. Not much is known about them, since they are hard to isolate (in two membranes, and some aqueous fluids). The nucleoporins allow some proteins to enter the nucleus through the nuclear pore, like histones, DNA polymerase, etc. All of these proteins are synthesized in the cytoplasm, and have to be trafficked to the nucleus. Lots of proteins, especially histones, have to be routed in right before cell replication. Lots of mRNA, rRNA, and regulatory proteins go out of the pores to the cytoplasm. The pores are like one-lane, two-way bridges, and each nuclear pore functions in import and export. They have to coordinate two-way traffic to avoid collisions. |
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Term
| nucleus localization signal |
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Definition
| NL signal. Allows proteins to be trafficked in by the nuclear pores. It might have one signal sequence, a linear sequence of amino acids, or it might have regions of linear amino acids that combine together to make a signal patch when the protein folds up. A signal sequence is easier to find and identify. You can lop off sections of the protein, and see if it still goes to the nucleus. If it stays in the cytoplasm, you know you disrupted the signal. |
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Term
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Definition
| float in the cytoplasm and recognize NL signal sequences and patches on newly-synthesized proteins, and bind to them. They escort the proteins through the nuclear pores. Many proteins within the nuclear pore have repeating sequences of phenylalanine-glycine (F-G) amino acids. If a gene is being sequenced and the amino acid code is being predicted to have repeating Fs and Gs, the gene might encode a nucleoporin protein. These repeating sequences and the nuclear import receptors serve to ratchet the protein quickly through the pore into the nucleus. Another molecule won’t go through the same nuclear pore at the same time. |
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Term
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Definition
| you remove a stretch of nucleotides from a gene that encodes a nuclear protein, or remove a series of amino acids from the protein, and the protein stays in the cytoplasm, you know that you disrupted part of the shipping label or NL. Then you see which sequence you cut out, and what amino acids it encodes. This shows that those amino acids are necessary for trafficking, but not that they are sufficient (that they alone will ensure trafficking, and no more off the sequence is needed). To see if they’re sufficient to transport the protein, you can attach that sequence to the gene that encodes a cytoplasmic protein, and see if that cytoplasmic protein now ends up in the nucleus. If it does goes to the nucleus, you know that that sequence is both necessary and sufficient. |
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Term
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Definition
| (Helper T cells, which are disrupted by HIV) Part of the adaptive immune system are activated. These cells turn on certain genes that change them so they can combat the infection. This activation is controlled by a nuclear import signal, a nuclear export signal, a protein kinase, and a protein phosphatase in cooperation. |
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Term
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Definition
| found on proteins and get proteins like regulatory proteins out of the nucleus. |
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Term
| Nuclear Factor of Activated T Cells (NF-AT) |
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Definition
| a protein that cycles between the cytoplasm and the nucleus, and therefore has both nuclear import and export signals. Inside the nucleus, this protein activates the transcription of certain genes. |
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Term
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Definition
| a protein phosphatase that needs to bind to Ca++ ions to function properly. It only lives in the cytoplasm, and therefore is only active when Ca++ concentration in the cytoplasm is higher than normal, so it’s inactive most of the time. |
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Term
| ionophore bacterial proteins |
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Definition
| will punch holes in the cell’s membranes to let Ca++ flow into the cells (bacteria use these proteins in warfare). Once Ca++ has flowed into the cell and increased the concentration in the cytoplasm, NF-AT will travel to the nucleus. When the ionophores degrade and go away, Ca++ will flow back out of the cell or into organelles like the ER, lowering the cytoplasmic concentration of Ca++. NF-AT will travel back out of the nucleus into the cytoplasm. Ionophores can be blocked, and will degrade quickly. They act as artificial ion channels. |
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Term
| T lymphocute activation pathway |
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Definition
| gets started when NF-AT is phosphorylated in the cytoplasm. Calcineurin is activated when Ca++ levels rise and it clips the phosphate groups off of the NF-AT to reveal a nuclear import signal that was hidden and blocked by the phosphates. NF-AT is imported through a nuclear pore to the nucleus, where it turns on some genes. As Ca++ levels lower, Calcineurin is deactivated and falls off of the NF-AT molecule, revealing a nuclear export signal. A kinase in the nucleus comes along and phosphorylates the NF-AT, hiding the nuclear export signal again. NF-AT is exported back out to the cytoplasm, where eventually Calcineurin will bind to it again and cover the nuclear export signal. |
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Term
| Retention in the ER lumen |
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Definition
| (at the C terminus. Proteins that get routed into the ER lumen will automatically keep going on to the Golgi and further if they do not have this sequence to retain them) |
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Term
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Definition
| S K L (at the C Terminus) |
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Term
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Definition
| Using 35S as a label ensures that only amino acids, and no other cellular components, are labeled. They let the starved cells feed on radioactive M for a few minutes (the pulse) and then gave them a huge excess of non-radioactive (cold) M (the chase). This makes it unlikely that any more radioactive M will end up in proteins, since there’s such a large amount of cold M in the cell, ending the pulse. They harvested some cells 0 minutes after adding the cold M, to see where the radioactive proteins were (they should still have been in the cytoplasm, having just been synthesized). They then sampled cells at various times after the start of the chase, to determine the location of the radioactive proteins at each time, and thereby track the protein’s route through the cell. |
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Term
| pancreatic epithelial cells |
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Definition
| secrete 80% of the proteins they produce. Used in pulse-chase experiments. |
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Term
| Signal Recognition Particle |
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Definition
| SRP. A cytoplasmic protein complex. The complex is made of 6 different protein subunits and 1 RNA molecule. When this complex binds to the newly emerging protein, it halts translation. The SRP goes to an integral membrane protein in the rough ER membrane, and binds to the receptor. This binds the whole ribosomal complex and the newly emerging protein to the rough ER membrane. The SRP receptor anchors the ribosomal complex over a protein translocator in the rough ER membrane called the Sec61 complex. |
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Term
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Definition
| A protein translocator in the rough ER membrane.The protein pauses in translation when it bind to the SRP and is brought to the rough ER membrane so that no more of it will emerge and begin folding in the cytoplasm, making it hard to route through. Sec61 routes the protein through the rough ER membrane into the lumen. When Sec61 isn’t in use, another protein plugs it. Proteins have to go through this process to get into the ER, and then they can go anywhere else in the cell.The protein being synthesized gets jammed into Sec61 so that it forms a hairpin, with the signal sequence pointing up into the membrane, and the newer part of the protein in the ER lumen. Translation starts again, and the protein gets synthesized across the ER membrane into the ER lumen. |
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Term
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Definition
| comes along and clips a peptide bond when the protein is done being translated, and the C terminus has come out,so that the signal sequence (which is still stuck in the ER membrane) gets clipped off. The signal peptidase does this by recognizing a cleavage site, certain sequence in the protein next to the signal sequence. It then catalyzes peptide bond hydrolysis. This means that the protein now has a new N terminus, and the first amino acid in the protein may not be an M. So if you find a protein that has an N terminus that isn’t an M, that means that part of the protein was clipped off at some point. This frees the protein into the ER lumen. an integral ER membrane protein. Its catalytic site sticks just barley out into the ER lumen, so that it can cut the peptide bond between the protein and the signal sequence. |
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Term
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Definition
| comes along and removes the signal sequence from the Sec61. The amino acids in the signal sequence are re-used elsewhere. |
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Term
| co-translational insertion |
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Definition
| insertion while translation is going on |
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Term
| Post-translational-insertion |
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Definition
| have to unfold a protein to insert it through a membrane. |
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Term
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Definition
| after will stop the movement of the protein through the membrane. So the protein will continue to be translated, but only on the side of the membrane where the ribosome is. So everything downstream of the stop-transfer sequence will be synthesized into the cytoplasm. This means that the C terminus is in the cytoplasm, and the N terminus is in the lumen. If there’s a stretch of more than 18 non-polar amino acids in a protein, this could indicate a stop-transfer sequence, and a transmembrane protein. The protein still has a signal sequence, but it will be eaten by signal peptide peptidase. must always have a start-transfer or signal sequence preceding it in the amino acid sequence. You can’t lead off with a stop-transfer sequence. A stop-transfer sequence can’t follow - + start-transfer sequence, because the protein synthesis is already happening in the cytoplasm. |
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Term
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Definition
| The amino acid sequence of an integral membrane protein dictate its topology in the ER membrane (and therefore in any other membrane it might travel to). If the protein needs to stay in the ER lumen, and not move on, it needs to have the sequence KKXX at its C terminus. The Xs are variable. If the protein only has a signal sequence and a stop-transfer sequence, it will automatically travel to the plasma membrane. Sec61 is a protein that lives in the ER membrane, so it must have a KKXX sequence on its C terminus. Once a protein is membrane-bound, it always will be. |
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Term
| internal start-transfer sequence |
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Definition
| is a kind of signal sequence that is inside the protein, and appears after part of the protein has already been synthesized in the cytoplasm. This internal start-transfer sequence will still bind to SRP and get guided to the ER membrane. The N terminus will be in the cytoplasm, unlike a simple signal sequence, where the N terminus ends up in the lumen. There is no signal sequence to be gotten rid of, so signal peptidase doesn’t cleave any peptide bonds, and it certainly doesn’t cut the internal start-transfer sequence, which will stay in the membrane like a stop-transfer sequence does. If an internal start-transfer sequence was put into the Sec61 complex backwards, this would mess up its topology, and it wouldn’t function right. The cell needs to know which end of the protein goes where. The more positively-charged end of the internal start-transfer sequence will always go in the cytoplasm. The negatively-charged end goes into the ER lumen. |
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Term
| a + - internal start-transfer sequence |
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Definition
| the N terminus (near the + end) will end up in the cytoplasm, and the C terminus (closer to the – end of the sequence) will be in the ER lumen |
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Term
| - + internal start-transfer sequence |
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Definition
| the sequence is inserted into the Sec61 complex with the – end first, so the N terminus ends up in the ER lumen, and the C terminus is in the cytoplasm. This gives the same result as a signal sequence followed by a stop-transfer sequence. So the protein downstream of the sequence remains in the cytoplasm until the protein is completely synthesized or a normal + - internal start-transfer sequence comes out of the ribosome. The only time you see a - + start-transfer sequence is near the beginning of a protein, and only once. |
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Term
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Definition
| The number of hydrophobic peaks indicates how many membrane-spanning regions there are. This allows you to make a model and test it. To test it, you can put the DNA for the protein into cells, and then burst them open and isolate the ER membrane to see which parts of the protein stick out of the microsomes, into the cytoplasm, and which parts are hidden in the lumen. You can design antibodies for certain regions of the protein, and then use them to see if the part you think is facing the cytoplasm actually is. You can detergentize the microsomes to see the insides, and see if the antibodies will bind there. |
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Term
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Definition
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Term
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Definition
| Coat vesicles from the ER, when the active Sar1 that is stuck in the membrane binds to COP II proteins, and a shell starts to form, pulling up the membrane with it. The COP II proteins will not bind to inactivated, cytoplasmic Sar1. When the vesicle is formed and needs to shed its coat, it inactivates Sar1 so that it and the COP II proteins pop off of the vesicle. COP II proteins can serve as GAPs, but they only deactivate Sar1 after the vesicle is fully formed |
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Term
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Definition
| Coat that bud from the Golgi and return to the ER are coated. |
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Term
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Definition
| Vesicles transport proteins along secretory pathways in vesicular transport. Vesicles are small, membrane-bound compartments that bud off of larger organelles and then travel to other organelles, or the cell surface, and merge with those membranes to deposit their cargo in a new location. Vesicles differ in their coating. The coating proteins bind to the lipids and then bind to each other to make a dome shape, which forces the membrane out into a dome, as well. Once the bud has completely split off into a vesicle, this coating is shed, so that it doesn't get in the way of any interactions. |
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Term
| Guanine-nucleotide exchange factor |
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Definition
| GEF) proteins bind to G-proteins and turn them on by clipping off a GDP and replacing with a GTP. |
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Term
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Definition
| a G-protein in the cytoplasm near the ER membrane. . Sec12 is the GEF that binds to and activates Sar1, causing it to pop out a hydrophobic tail (a conformational change). This causes the Sar1 to jam into the ER membrane next to Sec12. The active Sar1 that is stuck in the membrane binds to COP II proteins, and a shell starts to form, pulling up the membrane with it. The COP II proteins will not bind to inactivated, cytoplasmic Sar1. When the vesicle is formed and needs to shed its coat, it inactivates Sar1 so that it and the COP II proteins pop off of the vesicle. |
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Term
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Definition
| A protein within the membrane. The GEF that binds to and activates Sar1, causing it to pop out a hydrophobic tail (a conformational change). This causes the Sar1 to jam into the ER membrane next to Sec12. |
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Term
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Definition
| This is a cycle, where a g-protein (Sar1 or Ras) that is inactive gets activated by a GEF that breaks off a GDP and replaces with with a GTP on the g-protein. There’s lots of GTP in the cytoplasm, so more will bind opportunistically after the GDP has been clipped off. The active g-protein will go about its business until a GAP comes and removes a phosphate, making the GTP into a GTP and inactivating the g-protein. A cancerous Ras protein can’t have the phosphate group clipped off of the GTP, and will never be inactivated. |
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Term
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Definition
| works by going into a cell and degrading SNARE proteins. This messes up neural transport and causes respiratory paralysis (lockjaw). Tetanus selectively causes this degradation. |
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Term
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Definition
| integral membrane proteins. There are 3 SNARE proteins involved in a SNARE fusion. A v-SNARE in the vesicle binds to a t-SNARE in the target organelles, and a second, peripheral t-SNARE helps form the complex to anchor the vesicle to the target membrane. This allows the membranes to fuse, and the vesicular lumen to be dumped into the organelle’s lumen. |
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Term
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Definition
| are g-proteins that facilitate SNARE-to-SNARE interactions, and ensure that they’re accurate. Without Rab proteins, SNARE proteins wouldn’t bind and membranes wouldn’t fuse correctly. |
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Term
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Definition
| Proteins with the KDEL sequence at their C terminus are kept in the ER lumen. Sometimes they escape to the Golgi and have to be routed back to the ER. These proteins stow-away in vesicles destined for the Golgi. The KDEL proteins run into receptors in the cis-Golgi that bind to them. These KDEL receptors bind to COP I proteins in the cytoplasm, which coat the vesicles that go back to the ER. The G-protein ARF recruits COP I to make the coating of the vesicle (like SAR1). Once the vesicles reach the ER, the KDEL receptors need to let the KDEL protein off. The Golgi has a slightly acidic lumen, and the ER has a basic one, so the KDEL receptors have a high affinity for KDEL proteins in the slightly acidic Golgi, but this affinity lessens once they’re in the basic ER. The KDEL sequence of the protein has to be at the C terminus, it won’t work if it’s in the middle of the protein’s sequence. Some KDEL proteins manage to get all the way through the Golgi and escape, despite these measures. |
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Term
| default vesicular pathway |
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Definition
| consists of unregulated vesicles that run all day to the cell surface |
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Term
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Definition
| normally found in cells that secrete large amounts of a certain protein intermittently, when instructed to. In some cells, secretory vesicles travel a long way to poise just inside the plasma membrane until they’re needed. Secretory vesicles bud off from the trans-Golgi, and are coated with clathrin proteins. An immature secretory vesicle is only partially coated with clathrin. Parts of the immature vesicle that are coated in clathrins start to shrink and break off, forming small vesicles that are completely clathrin-coated. These vesicles go back to the trans-Golgi. The remaining part of the secretory vesicle, with no clathrins, has a high concentration of proteins now, and can dump more out of the cell at the right time. |
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Term
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Definition
| proteases called resident proteins make small peptides that serve as hormones or neurotransmitters. These proteins are cut apart into different substituents in different cells. The protein pro-opiomelanocortin is cut into two pieces in the cells of the pituitary anterior lobe, but it’s cut into four different pieces in the cells of the pituitary intermediate lobe. It’s hard to traffic small proteins, so it’s easier to traffic a large one through the cell and then cut it up near the end of its journey. |
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Term
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Definition
| These cells make huge amounts of histamine molecules, and store these molecules in secretory vesicles under the cell surface. When a stimulatory molecule binds to a receptor on the cell surface, the cell dumps all the histamine into the bloodstream. This can cause problems such as high blood pressure, constricted blood vessels. |
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Term
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Definition
| If all a zygote had for inherited information was DNA, how would the proteins encoded by this DNA finding the locations that their shipping labels tell them to go to? The DNA contains the address the proteins need to go to, but the streets and numbers of the destination organelles have to be supplied by molecules already positioned in the egg cell. You have to have a cell to begin with, to make an organism, so everything will be in place to direct proteins to where they must go. |
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Term
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Definition
| Cholesterol molecules make membranes thicker, by stabilizing the fatty acid tails of phospholipids. The plasma membrane and vesicles from the trans-Golgi are rich in cholesterol. This makes them thicker than the membranes of other organelles. Proteins have different lengths of transmembrane regions. Proteins in the ER and Golgi, which have skinnier membranes, have shorter membrane-spanning regions (15-18 non-polar amino acids) than proteins found in the secretory vesicles and plasma membrane (20-30 amino acids). So the length of a protein’s membrane spanning region determines what membrane it will end up in. |
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Term
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Definition
| used to help keep organelle proteins in the lumen, and out of departing vesicles. This happens when the luminal proteins have homotypic binding, where they bind to other protein molecules of the same kind. They bind at their N terminus to a similar protein’s C terminus. The aggregates that this forms are too big to fit into departing vesicles, and this keeps the protein in that compartment. This behavior depends on variables such as the pH of the protein’s destination organelle. Proteins that need to stay in the Golgi won’t exhibit hemolytic binding until they reach the Golgi ad the pH is lower than that of the ER. |
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Term
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Definition
| All the membranes in a cell are dynamic, but the plasma membrane is more distinctive than the other membranes. There are subdomains in the plasma membrane of different phospholipids, which form lipid rafts. These lipid rafts contain proteins important to cell communication. |
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Term
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Definition
| . Acid hydrolases cleave bonds by bringing a molecule of H2O in, for hydrolysis. There are many different types of acid hydrolases, all specialized to cleave particular kinds of bonds.When these molecules are broken down by acid hydrolases, they produce amino acids, nucleotides, sugars, and other small molecules, which are transported out of the lysosome for re-use. Each of these different acid hydrolases is indispensable to the functioning of the cell, since they are so specific in the molecules they break down. |
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Term
| lysosomal storage disease |
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Definition
| If an acid hydrolase protein is missing in a cell do to an allele being homozygotic or due to a mutation.caused by one or more missing lysosomal enzymes, which may not have been made or trafficked correctly. |
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Term
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Definition
| a lysosomal storage disease, where infants suffer from being blind or deaf, and often die by the age of 3. This is caused by the buildup of gangliosides, a kind of lipid, in the neurons of the brain. These gangliosides are normally broken down by a specific lysosomal protein, but if that protein is missing, then it causes the disease. |
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Term
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Definition
| . New phospholipids have to be brought in constantly, to replace ones that are eaten up. Entire lysosomes have to be replaced continually, since they get eaten up. |
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Term
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Definition
| Endocytosis occurs when part of the plasma membrane of the cell gets pulled into the cell to form vesicles (usually clathrin-coated). These vesicles contain molecules from the extracellular fluid. This process is like vesicular budding, but backwards. These vesicles fuse with early endosomes floating in the cytoplasm. These early endosomes need to have their pH gradually lowered and acid hydrolases pumped in from the Golgi. As this process goes on, they mature into late endosomes and finally lysosomes. This process of endocytosis and endosomal maturation is continual. |
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Term
| Trafficking acid hydrolases |
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Definition
| ? First, they have to have a signal sequence, to be routed into the ER lumen via co-translational transmembrane transport. These proteins have a special asparagine in a special context within the protein that allows proteins in the ER lumen to attach an oligosaccharide to the hydrolase. The oligosaccharide is N-linked (a sugar attached to a Nitrogen atom) to the protein, and a 6-carbon mannose sugar is attached to this oligosaccharide. The protein travels to the Golgi, where a carbohydrate kinase attaches a phosphate to the mannose, making it mannose 6-phosphate (M6P). |
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Term
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Definition
| A phosphate on a mannose. The primary tag on the hydrolase is the asparagine, and the mannose 6-phosphate acts as the shipping label. When the protein gets to the trans-Golgi, mannose 6-phosphate receptor proteins in the Golgi membrane attach to the M6P on the hydrolase and bud off into clathrin-coated vesicles. The M6P receptors have an affinity for clathrin. |
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Term
| Mannose 6-phosphate receptor proteins |
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Definition
| in the Golgi membrane attach to the M6P on the hydrolase and bud off into clathrin-coated vesicles. The M6P receptors have an affinity for clathrin. The vesicles travel along and fuse to a late endosome, where they lose their affinity for the hydrolase, because the pH is lower in the late endosome. The receptors dump the proteins out into the late endosome and bud off again in a different vesicle to travel back to the trans-Golgi, where they are re-used. The returning vesicle from the late endosome has a low pH, so when it fuses back with the Golgi, it lowers they pH of the trans-Golgi slightly. Once inside the late endosome, a phosphatase comes along and clips the phosphate off of the mannose, so that the M6P receptors won’t rebind to the hydrolase and carry it out of the late endosome. This is a very efficient process, where proteins only have to be delivered once, and receptors are re-used. |
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| One of the primary functions of lysosomes is the degradation and processing of molecules from outside of the cell that are carried in via endocytosis. The lysosomes break these extracellular molecules down into monomers so that they can be used for other things. Clathrin proteins live in the cytoplasm, but it becomes peripheral on the inside of the plasma membrane. These proteins make a clathrin-coated pit on the inside of the membrane to pull a vesicle in. |
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| . To reduce this synthesis to a trickle (to make the cell pick up more LDL from the bloodstream), but not to stop the synthesis of other molecules (like ubiquinone) in this pathway. HMG-CoA reductase is the enzyme that is usually down-regulated. If you have high cholesterol, you want to take a drug that targets this protein. ). You want a dose that’s high enough to make cholesterol production decrease and LDL intake increase. If the LDL receptors are defective (they don’t end up in the clathrin-coated pits), this can cause high LDL concentration in the bloodstream. Shutting down cell cholesterol synthesis will make the cell make more LDL receptors to get cholesterol from the bloodstream, and these receptors will overpopulate the plasma membrane so that at least some work and get caught in the clathrin-coated pits. |
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| On the surface of cells that need LDL. These receptors bind to LDL, but they also have a special shape that allows them to bind to the clathrin-coated pits. This means that there’s a dense concentration of LDL receptors in the pits, so when the pits form vesicles, the LDL will be pulled inside the cell. The vesicle fuses with an early endosome, and the LDL gets dumped in to get de-esterified. The receptors get separated back out into a recycling vesicle, which goes back to the cell surface to re-use the receptors. |
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| Family Hypercholesterolemia |
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| Disease where kids have high levels of LDL in their bloodstream, because their cells don’t internalize LDL correctly. This is because the LDL receptors don’t bind properly to adaptin, which is the protein that hooks the LDL receptors to the clathrin. This means that when clathrin-coated pits form, the receptors don’t gather in the pits to get taken into the cell. The receptors bind to the LDL, but they never get taken into the cell, so eventually the LDL disintegrates and the cholesterol molecule bind to the artery walls. Lipitor shuts down the cell’s cholesterol pathway (which has been working overtime) down, so that the cells are desperate for cholesterol. The cells ramp up the synthesis of the LDL receptors, so that the cell surface is covered in them. Whenever a clathrin-coated pit occurs, a few LDL receptors are bound to end up in there, even if they aren’t actually bound to the adaptin proteins. This way LDL is taken out of the bloodstream and into the cells. Lipitor inhibits the rate-determining (slowest) enzyme in the cholesterol synthesis pathway. This enzyme is found in the ER membrane, with the catalytic end in the cytoplasm. It’s easy to clip off and study the catalytic end, so an inhibitor can be developed. There aren’t many side effects. |
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| Allow some cell surface proteins to be maintained as “on-demand” for certain cellular functions. |
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| needed for glucose from food to cross the plasma membrane into the cell. |
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| on the surface of the cell bind to insulin, which is produced in the beta-pancreatic cells. On stimulation due to the binding of insulin to the insulin receptors, glucose transporters contained in recycling endosomes go to the plasma membrane so that the cell can bring more glucose in, and faster. Glucose is a sugar, and polar, so it can’t cross the plasma membrane freely. The concentration of glucose is greater within the cells, so more glucose needs a special transporter to get into the cell. The glucose transporters make the recycling endosomes increase in concentration near the cell surface when insulin binds to insulin receptors, triggering their transport to the plasma membrane. |
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| occurs when not enough insulin is made in the beta-pancreatic cells, even when the levels of glucose in the blood were high. This means that glucose gathers in the blood and causes problems. To prevent this, shots of recombinant insulin from bacterial colonies can be taken. is caused by a missing population of beta-pancreatic cells. It would be possible to put a capsule that contains beta-pancreatic cells into the bloodstream. This capsule would have to have holes to let the insulin from the beta-pancreatic cells out and energy molecules in, but the holes would have to be small enough that the cells from the immune system can’t get in to get rid of the foreign cells. This doesn’t work so well in practice, because the immune system cells just gather around the holes and clog them up, so that insulin can’t go anywhere. |
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| comes more from lifestyle factors. The level of insulin is fine, but there’s something wrong with machinery used to get glucose into the cells (perhaps a receptor is mutated, or the transporters don’t get to the membrane). You can’t take sots to fix this. The effects tend to look like the effects of Type I after a while, as the glucose levels in the bloodstream rise. The effects are more gradual, though. The insulin receptors might get overstimulated and leave the cell surface, if you eat too much sugary or fatty food and this might cause Type II. The only way to regulate Type II is through diet. They are trying to figure out drugs for it. |
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| Lysosomes have another feature where they engulf other cells (like invading bacteria, or old, dysfunctional cells) and destroy them to re-use that cell’s pieces. This happens when a vesicle called a phagosome buds off of the inside of the plasma membrane, containing a cell. This cell inside the phagosome is brought to the lysosome, where the phagosome merges and dumps the cell into the lysosome to be broken down. This raises the lysosomes pH temporarily, since the cell that is being digested has a pH of 7.4. But the proton pumps on the lysosomes membrane pump more acidic protons in to restore the pH. |
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| major histocompatibility complex |
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| An antigen that, and if it is missing from the outside of a cell, the cell will get eaten. |
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| post-translational transmembrane transport |
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| Most of the proteins in the mitochondria have to be trafficked in after they’re translated, directly from the cytoplasm and not through a vesicle. These proteins have to be unfolded and spooled across the mitochondrial membrane. Heat-shock proteins, specifically HSP70 and HSP40, bind to the proteins and stabilize them while they get routed across the membrane. HSP proteins are in the chaperone class, and they allow proteins to withstand heat as part of heat shock response. They also allow proteins to unfold and snake across membranes through trans-membrane proteins to reach their destination. |
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| In the mitochondrial outer membrane.These allow free diffusion on molecules that are 5000 Daltons or less into and out of the mitochondria. This means that there is no ion gradient between the intermembrane space of the mitochondria and the cytoplasm. |
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| found exclusively in the inner mitochondrial membrane. It has 4 fatty acid tails, instead of just 2, and 2 phosphates. This makes it harder for ions to cross the inner membrane. |
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| The F0 part of the complex is in the inner mitochondrial membrane, and the F1 complex is in the matrix and is better studied. The rotor is the record turning, and the stator is the needle. Both are in both complexes. The H+ bind to the rotor subunits and drive the rotor by inducing conformational changes. The rotor turns around through the membrane with the H+ bound to it. Once the protons reach the beginning, they go down a special channel in the stator and pop out into the matrix. The energy from the rotation of the rotor goes to the shaft in the rotor, and changes the protein conformation in the bottom of the stator. This change makes ADP into ATP. The central shaft affects the shape of the subunits and drives ATP synthesis. |
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| Difficult to isolate from the ER, when fractionating cells. The site of most carbohydrate synthesis in the cell, so it has a lot of proteins for carbohydrate synthesis catalysis. Site of oligosaccharide addition to certain proteins, to make glycoproteins. The ER can also attach carbohydrates. This is done by recognizing and adding on to certain amino acid sites. It distributes all to proteins imported from the ER. If a protein wants to leave the cell, it must go through the Golgi. The size can be variable, and it has a larger volume in cell specialized for secretion, like B-lymphocytes (which secrete a lot of antibodies). It contains structural matrix proteins that are phosphorylated during mitosis, allowing the Golgi to disperse quickly and temporarily. These proteins have a coiled-coil domain, which gets phosphorylated at the beginning of mitosis. This disperses the Golgi, and the dephosphorylation of these proteins at the end of mitosis causes the Golgi to come back together again. |
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