Term
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Definition
| ties nucleosome beads together |
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Term
| what characterizes heterochromatin? |
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Definition
| highly condensed - not transcriptionally active |
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Term
| what characterizes euchromatin? |
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Definition
| less condensed - transcriptionally active |
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Term
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Definition
| adenine guanine - PUR As Gold |
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Term
| what are the pyrimidines? |
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Definition
| cytosine thymine uracil - CUT the PY |
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Term
| what are the AAs necessary for purine synthesis? |
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Definition
| glycine, aspartate, glutamate |
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Term
| what are purines made from? |
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Definition
|
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Term
| what are pyrimidines made from? |
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Definition
| orotate precursor w/PRPP added later |
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Term
| what does hydroxyurea inhibit? |
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Definition
|
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Term
| what does 6-mercaptopurine inhibit? |
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Definition
| blocks de novo purine synthesis |
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Term
| what does 5-fluorouracil block? |
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Definition
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Term
| what does methotrexate inhibit? |
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Definition
|
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Term
| what does trimethoprim inhibit? |
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Definition
| bacterial dihydrofolate reductase |
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Term
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Definition
| inability to convert orotic acid to UMP (de novo pyrimidine synthesis pathway). autosomal recessive. findings: increased orotic acid in urine, megaloblastic anemia, failure to thrive. no hyperammonemia. tx: oral uridine administration. |
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Term
| what happens w/an adenosine deaminase deficiency? |
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Definition
| excess ATP and dATP = imbalances the nucleotide pool via feedback inhibition of ribonucleotide reductase. this prevents DNA synthesis and thus decreases lymphocyte count. **one of the major causes of SCID. SCID happens to kids. |
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Term
| what is lesch-nyhan syndrome? |
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Definition
| a defect in purine salvage - owing to the absence of HGPRT (He's Got Purine Recovery Trouble), which converts hypoxanthine to IMP and guanine to GMP. this results in excess uric acid production. X-linked recessive. findings: retardation, self-mutilation, aggression, hyperuricemia, gout, and choreoathetosis. |
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Term
| what is degenerate/redundant genetic code? |
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Definition
| more than 1 codon may code for the same amino acid. exception: methionine is encoded by only 1 codon: AUG |
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Term
| what is a nonsense mutation? |
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Definition
| a change resulting in an early stop codon (stop the nonsense!) |
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Term
| what is a missense DNA mutation? |
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Definition
| changed AA to something similar |
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Term
| what is a silent mutation? |
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Definition
| same AA, often the base changes in the third position of the codon - tRNA wobble |
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Term
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Definition
| unwinds the DNA template at the replication fork |
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Term
| what does DNA topoisomerase do? what antibiotic class is related? |
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Definition
| creates a nick to help relieve supercoils created during replication. fluoroquinolones inhibit DNA gyrase, a prokaryotic specific topoisomerase). |
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Term
| what is primase? what is DNA polymerase III? |
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Definition
| this makes an RNA primer on DNA polymerase III - which can initiate replication. DNA polymerase III is prokaryotic only. it elongates the lagging strand (5'->3') until it reaches the primer of the preceding fragment. it also has 3'->5' exonuclease activity which proofreads each added nucleotide. |
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Term
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Definition
| prokaryotic only. degrades RNA primer and fills in the gap w/DNA w/5'->3' exonuclease. |
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Term
| what characterizes nucleotide excision repair? what happens if this is mutated? |
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Definition
| specific endonucleases release the oligonucleotide-containing damaged bases. DNA polymerase and ligase fill and reseal the gap respectively. if this is mutated = xeroderma pigmentosum (prevents repair of thymidine dimers). |
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Term
| what characterizes base excision repair? |
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Definition
| specific glycosylases recognize and remove damaged bases, AP endonuclease cuts DNA at apyrimidinic sites, the empty sugar is removed and the gap is filled and resealed. |
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Term
| what characterizes mismatch repair? what can happen if this process is messed up? |
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Definition
| an unmethylated, newly synthesized string is recognized, mismatched nucleotides are removed and the gap is filled and resealed. this is mutated in HNPCC. |
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Term
| what direction are both DNA and RNA both synthesized? |
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Definition
| 5'-3'. the 5' of the incoming nucleotide bears the triphosphate (energy source for the bond). the 3' is the target for the 3' hydroxyl attack - drugs blocking DNA replication often have modified 3' OH, preventing addition of the next nucleotide (chain termination). |
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Term
| what is the mnemonic for RNA types? |
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Definition
| Rampant (rRNA: most abundant), Massive (mRNA: longest), Tiny (tRNA: smallest) |
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Term
| what is the mRNA start codon? |
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Definition
| AUG (inAUGurates). in eukaryotes: codes for methionine (may be removed). in prokaryotes: codes for formyl-methionine. |
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Term
| what are exons vs introns? |
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Definition
| exons are on the outside of the coding region in DNA and introns on on the inside. INtrons are INtervening sequences which stay IN the nucleus, whereas EXons EXit and are EXpressed. |
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Term
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Definition
| a stretch of DNA which alters gene expression by binding transcription factors. |
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Term
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Definition
| the site where negative regulators (repressors) bind |
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Term
| what is the naming sequence for RNA polymerases in eukaryotes? |
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Definition
| RNA polymerase I: makes rRNA, RNA polymerase II: makes mRNA (alpha-amanitin found in death cap mushrooms inhibits this = liver failure), RNA polymerase III: makes tRNA. |
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Term
| where does RNA processing occur in eukaryotes? |
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Definition
| in the nucleus. after transcription, the 5' end is capped (7-methyguanosine) and the 3' end undergoes polyadenylation (~200 AA's, AAUAAA: polyadenylation signal). introns are spliced out. the initial transcript is called hnRNA, then once capped+tailed = mRNA. once, processed, RNA can be transported out of the nucleus. |
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Term
| who does pre-mRNA splicing occur in? how does this occur? what disease is related to this process? |
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Definition
| eukaryotes. the primary transcript combines w/SNRPs and other proteins to form the spliceosome. this forms an intermediate lariat loop and the intron is removed/exons are joined. pts w/lupus make Ab to splicesomal snRNPs |
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Term
| what do all tRNAs (both eukaryotic/prokaryotic) have? |
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Definition
| a CCA at the 3' end along w/a high percentage of chemically modifiable bases. the AA is covelently bonded to the 3' end of the tRNA. |
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Term
|
Definition
| amninoacyl-tRNA synthetase scrutinizes AA before and after it binds to tRNA. the bond is hydrolyzed if incorrect. the AA-tRNA bond has energy fro the formation of the peptide bond (ATP - Activation). a mischarged tRNA reads usual codon, but inserts the wrong AA. **tetracyclines bind the 30s subunit - preventing attachment of the aminoacyl-tRNA. |
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Term
|
Definition
| accurate base pairing is only required in the 1st 2 nucleotide positions of an mRNA codon, so codons differing in the 3rd "wobble" position may code for the same tRNA/AA. |
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Term
| what characterizes initiation phase of protein synthesis? difference between eukaryotes/prokaryotes? |
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Definition
| this is activated by GTP hydrolysis (GTP - Gripping/Going places). initiation factors (eIFs) help assemble the 40S ribosomal subunit w/the initiator tRNA and then are released when the mRNA and ribosomal subunit assemble w/the complex. eukaryotes: 40S + 60S -> 80S (EVEN). prokaryotes: 30S + 50S -> 60S (ODD). |
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Term
| what characterizes elongation phase of protein synthesis? |
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Definition
| 1) aminoacyl-tRNA binds to A site (Activation), except for initiator methionine). 2) ribosomal rRNA (ribozyme) catalyzes peptide bond formation and transfers the growing polypeptide to AA in the A site. 3) ribosome advances 3 nucleotides toward the 3' end of the RNA, moving peptidyl RNA to the P site (translocation). *going APE: A site (incoming Aminoacyl tRNA), P site (accomodates the incoming Peptide), and E site (holds Empty tRNA as it Exits) |
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Term
| what characterizes termination phase of protein synthesis? |
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Definition
| the stop codon is recognized by the release factor and the completed protein is released from the ribosome |
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Term
| what is the posttranslational modification "trimming"? |
|
Definition
| removal of N- or C-terminal propeptides from zymogens to generate mature proteins. |
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Term
| what are the covalent alteration posttranslational modifications? |
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Definition
| phosphorylation, glycosylation, and hydroxylation |
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Term
| what is the posttranslational modification: degradation? |
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Definition
| attachment of ubiquitin to the defective proteins to tag them for breakdown |
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Term
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Definition
| G1 (can slip into G0) -> S (synthesis) phase -> G2 -> mitosis -> G1. interphase: G1,S,G2 |
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Term
| what do Rb and p53 usually do? |
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Definition
|
|
Term
| what is a permanent cell? |
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Definition
| remains in G0, regenerates from stem cells - neurons, skeletal, cardiac and RBCs |
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Term
| what is a stable/quiescent cell? |
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Definition
| these cells will enter G1 from G0 when stimulated - hepatocytes, lymphocytes |
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Term
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Definition
| never go to G0, divide rapidly w/a short G0 - bone marrow, gut epithelium, skin, hair follicles |
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Term
| what characterizes the rough endoplasmic reticulum? attached vs free ribosomes? |
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Definition
| this is the site of synthesis of secretory (exported) proteins and of N-linked oligosaccharide addition to many proteins. nissl bodies (RER in neurons) synthesize enzymes and peptide neurotransmitters. mucus-secreting goblet cells of the small intestine and Ab-secreting plasma cells are rich in RER. **free ribosomes, which are unattached to any membrane are the sites of synthesis of cytosolic and organellar proteins. |
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Term
| what characterizes the smooth endoplasmic reticulum? |
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Definition
| this is the site of steroid synthesis as well as detoxification of drugs/poisons. liver hepatocytes and steroid hormone-producing cells of the adrenal cortex are rich in SER. |
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Term
| what characterizes the golgi apparatus? |
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Definition
| this is the distribution center of proteins/lipids from the ER to the plasma membrane, lysosomes and secretory vesicles. the golgi modifies N-oligosaccharides on asparagine, adds O-saccharides to serine and threonine residues, adds mannose-6-phosphate to specific lysosomal proteins (*targets the protein to the lysosome), conducts proteoglycan assembly from core proteins, and sulfates sugars in proteoglycans/selected tyrosine on proteins. |
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Term
| what is the vesicular trafficking protein: COPI? |
|
Definition
|
|
Term
| what is the vesicular trafficking protein: COPII? |
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Definition
| anterograde, RER -> cis-golgi |
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|
Term
| what is the vesicular trafficking protein: clathrin? |
|
Definition
| trans-golgi -> lysosomes -> plasma membrane -> endosomes (for receptor-mediated endocytosis) |
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Term
|
Definition
| inclusion cell disease is an inherited lysosomal storage disorder, a failure of addition of mannose-6-phosphate to lysosome proteins (enzymes are secreted outside the cell instead of being targeted to the lysosome). this results in coarse facial features, clouded corneas, restricted joint movement and high plasma levels of lysosomal enzymes. often fatal in childhood. |
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Term
|
Definition
| composed of helical polymerized alpha/beta tubulin. each dimer has 2 GTP bound. |
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Term
| what are the molecular motor proteins? |
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Definition
| these transport cellular cargo toward the opposite ends of microtubule tracks. dynein = retrograde to microtubule (+ -> -), kinesin = anterograde to microtubule (- -> +) |
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Term
| what drugs act on microtubules? |
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Definition
| mebendazole/thiabendazole (antihelminthic), griseofulvin (antifungal), vincristine/vinblastine (anti-CA), paclitaxel (anti-breast CA), and colchicine (anti-gout). |
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Term
| what is chediak-higashi syndrome? |
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Definition
| a microtubule polymerization defect resulting in decreased phagocytosis = recurrent pyogenic infections, partial albinism, and peripheral neuropathy. |
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Term
| what is the cilia structure in microtubules? what is kartagener's syndrome? |
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Definition
| 9+2 arrangement. 9 cilia doublets going peripherally circular are linked by axonemal dynein ATPase - which causes bending of the cilium by differential sliding of the doublets. kartagner's syndrome is a disorder where the cilia of microtubles are immotile due to a dynein arm defect. this results in male/female infertility, bronchiectasis, and recurrent sinusitis, and situs inversus. |
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Term
| what cytoskeletal elements are present in microvilli, muscle contraction, cytokinesis, and adherens junctions? |
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Definition
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Term
| what cytoskeletal elements are present in cilia, flagella, mitotic spindles, neurons and centrioles? |
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Definition
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|
Term
| what cytoskeletal elements are present in vimentine (connective tissue), desmin (muscle), cytokeratin (epithelial cells), gilial fibrillary acid proteins (neuroglia), and neurofilaments (neurons)? |
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Definition
|
|
Term
| what is the plasma membrane composed of? |
|
Definition
| an asymmetric lipid bilayer = 50% cholesterol/50% phospholipids, sphingolipids, glycolipids, and proteins. |
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Term
| what happens for every ATP consumed by the Na+K+ ATPase? what drugs affect this? |
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Definition
| 3 Na+ go out/2 K+ come in. *ouabain inhibits by binding to the K+ site. *cardiac glycosides directly inhibit the Na+/K+ ATPase, which leads to indirect inhibition of Na+/Ca++ exchange. |
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Term
| what is the mnemonic for the collagen types? |
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Definition
| Be So Totally Cool, Read Books. type I: bone/skin/tendon (bONE). type II: cartilage (carTWOlage). type III: Reticulin. type IV: basement/basal lamina (under the floor). |
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Term
| what comprises collagen synthesis inside fibroblasts? |
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Definition
| 1) synthesis (RER, alpha chains/*preprocollagen is translated [usually gly-X-Y polypeptide]). 2) hydroxylation (of specific proline/lysine residue - requires *vit C). 3) glycosylation (of pro-alpha-chain lysine residues and formation of *procollagen [triple helix of 3 collagen alpha chains]). 4) exocytosis (of procollagen into the extracellular space). |
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|
Term
| what comprises collagen synthesis outside fibroblasts? |
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Definition
| 1) proteolytic processing (cleavage of terminal regions of procollagen transforms it to insoluble *tropocollagen). 2) reinforcement of many staggered tropocollagen molecules by covalent lysine-hydroxylysine cross-linkage (by lysyl oxidase) to make *collagen fibrils. |
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|
Term
| what is ehlers-danlos syndrome? |
|
Definition
| faulty collagen synthesis (usually type III), causing *hyperextensible skin, *tendency to bleed, and *hypermobile joints. |
|
|
Term
| what is osteogenesis imperfecta? |
|
Definition
| a genetic bone disorder caused by a variety of gene defects. most common: autosomal dominant w/abnormal type I collagen - causing multiple fractures w/minimal trauma (may be during birth process), blue sclerae (translucent connective tissue over chroid), hearing loss (abnormal middle ear bones), and dental imperfections. |
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|
Term
| what is alport's syndrome? |
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Definition
| this is due to a variety of gene defects resulting in abnormal type IV collagen, usually X-linked recessive. characterized by progressive hereditary nephritis, deafness, and ocular disturbances. |
|
|
Term
| what is elastin? what 2 diseases involve it? |
|
Definition
| a stretchy protein w/in the lungs, large arteries, elastic ligaments, vocal cords, and ligamenta flava. it is rich in proline/glycine. it is formed of tropoelastin w/fibrillin scaffolding and may be broken down by elastase. marfan's is due to a defect in fibrillin. emphysema can be caused by an alpha-1 antitrypsin deficiency = excess elastase activity. |
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