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biochem test 3 2011
biochem and mol bio
| Question | Answer |
|---|---|
| Where do most of our nucleotides come from? | 95% de novo synthesis, only ~5% from diet can be utilized b/c rest are broken down in digestion |
| How is purine metabolism regulated? | feedback inhibition by products. regulates 3 different enzymes PRPPP being the first |
| Lesch-Nyhan is caused by a deficiency in? What are the symptoms? | caused by a deficiency in HGPRT. causes hyperuricemia, increase in uric aciduria. Juvenile onset of gouty arthritis, uric acid stone formation. Severe=brain damage, tendency for self mutilation. |
| How does alopurinol treat Gout? | Gout is caused by an increase in uric acid. Alopurinol blocks uric acid production at 2 steps (xanthine oxidase) Gout usually presents in the big toe for the first time. It can cause bone damage |
| SCIDS aka Bubble Boy | severe combined imunodeficiency syndrome. deficiency of deletion of adenosine deaminase. Inherited= profound lymphocyte deficiency. lack cellular and humoral immune fxn. |
| Why are there no real problems asscoiated with Pyrimidine metabolism? | degredation products are water soluble. beta-alanine and beta-aminoisobutyrate |
| What ratio should purines and pyrimidines be synthesized in? How do the 2 paths communicate? | 1:1 synth. crosstalk between paths via PRPP from purines activates CPSII for pyrimidine synthesis |
| What does ribonuclease reductase (RR) do? | nucleotides --------->deoxynucleotides Regulated at 3 sites. on/off reg, specificity, and via active sites. high levels of dADP shut it off |
| What does the dUMP rxn do? | dUMP--->dTTP. it is a "one carbon" reaction. requires folic acid. |
| Glycosylation takes place in the ER and golgi. What are some functions of the carbohydrate moiety in a glycoprotien? | targeting, recognition and resistance to proteolysis. |
| What is a glucoronide that we should already be real familiar with? | UDP-glucoronate...bilirubin diglucoronide...the addition of a glucoronate addds a neg charge and allows to be secreted due to increased solubility. Also cool b/c you can get Lactose without ingesting galactose via UDP-glucose (only in lactating mam's) |
| What would a deficiency in glucoronyl transferase increase? | indirect bilirubin. |
| What is a glucoronide that we should already be real familiar with? | Criggler-Najar is a reduction or absence of glucoronyl transferase. result in kernicterus (bilirubin in the brain) and death. |
| Gilbert's syndrome is also a deficiency in glucoronyl transferase but much milder. | someone may present with slightly elevated bilirubin levels, but nothing is really wrong. May be more sensitive to certain drugs |
| Hyaluronic acid is a? | GAG aka Mucopolysaccharide. Negatively charged, attract water and usually viscous like synovial fluid. |
| What do you need to remember about proteoglycans? | chondroitin sulfate dermatan sulfate heparan sulfate |
| I-cell disease | happens when proteins are mis targeted, the is no longer sufficient enzymes in the lysosomes to degrade the proreins that are there, so they build up and create "inclusions" |
| What are 2 lysosomal storage diseased associated with muccopolysaccharides? | Hunter and Hurler syndromes, Hunter is X LINKED. Diagnostically, look for dermatan sulfate or heparan sulfate in urine |
| Sphingolipidoses. There are several. | Gaucher is the most common. Fabry disease is X-Linked. Gaucher, Tay Sachs, and Neiman Pick are more common among Ashkenazi Jews (eastern european descent) |
| RAS, G proteins, MAPK, ERK, myc are some examples of? | proto-oncogenes, they are normal functioning cells but problems can occur with mutations, usually a "gain of function" |
| Tumor supressors do what? | stop cell growth, if something goes wrong they can no longer regualte cell growth, ie a car with no brakes. Some examples are p16, p53, p21, pRB, and pro apoptotic proteins(The oncogene is a stuck accelerator) |
| what is contact inhibition? | one way that cells limit their own growth, and obviously a potential place for a problem if they lose contact inhibition. |
| 6 ways that normal cells get transformed to cancer cells. | 1. sustained angiogenisis. 2.self sufficiency in growth signals. 3.insensitivity to anti growth signals. 4.Evasion of apoptosis. 5.immortality. 6.tissue invaion and metastatsis |
| 8 or so types of proto-oncogenes | 1.growth factors 2.growth factor receptors 3.Sig transduction proteins 4.G proteins 5.PKA, PKC ...6.transcription factors 7.anti apoptotic cells |
| Mutations in coding regions, which can cause the production of a hyperactive protein, and Gene rearrangement, where you can then have a strong promoter controlling are 2 ways that proto-oncogenes can become oncogenes. What one more way? | if you express multiple copies of the same protein=Gene amplification |
| Functionally what type of mutation happens with tumor supressors? | Loss of function. Know BRCA1 and BRCA2 (caretaker genes) |
| Tumor supressors are involved in? | cell division, replication, and apoptosis |
| At what phase of theh cell cycle is the "control point" for most tumor supressors? | G1 mostly going to S phase |
| What do cyclin D's do? | bind to cyclin dependent kinases and help control check points. Activated by growth factors. |
| When cyclin D binds CDK it hyperphosphorylates RB which dissociates from E2F-->cyclinE...CyclinA...finally DNA synthesis. How is this controlled? | When it works p53 which acts as a beacon,brings in GADD 45 to fix damage, and serves to activate p21. p21 shuts down cyclin D, which cant hypophos4late RB so RB and E2F stay bound=inactive. System is shut down till DNA is repaired. Major Control Point** |
| What is E2F? | a transcription factor |
| Retinoblastoma the only cancer griffith knows of caused from a sinlge mutation. It is a mutaition in what gene? | RB, no shit, chromosome 13. |
| All I know about RAS at this point (havent studied Thatcher yet) is... | RAS as an oncogene is going to be because of a mutation in GTPase so that it is always on, this will drive proliferation of everything downstream. |
| HER2 is involved in? | breast cancer. a mutation from valine to glutamine, receptors will be active and perpetually phosphorylated this activates the signal transduction pathway. |
| From the standpoint of the human, what would you want more of, Bax of Bcl2? | Bax for sure. pro apoptotic. Bcl2 good for cancer , bad for humans. Bcl2 is expressed in 70% of breast cancer, b/c an overexpression of Bcl2 allows evasion of apoptosis. |
| All cancers have to avoid apoptosis, how would you design a drug to deal with this? | formulate a drug that binds Bcl2 so that Bax can do its thing. |
| When cancer is metastasizing what does it use to pull cells inside? | invadopodia |
| How does the multiple hit hypothesis support the fact that cancer is more prevelant as we age? | It takes time to accumulate the "hits" ie different mutation that all culminate in cancer. you also need mulitiple hits because there are multiple paths and multiple "checkpoints" that need to be bypassed |
| What happens to telomeres everytime you replicate? | they lose some basepairs till finally they can no longer replicate. reached senescense, the stoplight for cell division. they are then targeted for degredation. |
| Why does this not happen to cancer cells? | All cells have telomerase, cancer cells just turn it on. It gives them immortality, meaning they can divide indefinately(same as embryonic stem cells) |
| What is overexpressed in 90% of cancer cells? | telomerase |
| Burkett Lymphoma? | myc over expression (it is a transcription factor). translocation of chr. 8 and 14 |
| Why do we treat cancer with 5-flourouracil? | it inhibits the dUMP reaction so no TTP means it will slow down cell growth. |
| Chronic myelogenous leukemia (CML) | translocation of chr9 and 22 (philadelphia chromo)caused by a mutation in a tyrosine kinase receptor |
| The blots named after compass points all started with? | Southern blot-DNA sequences |
| Then came a blot that hyvridized RNA with DNA, what direction is it? | Northern blot. And finally the Western Blot is used for proteins, this teechnique utilizes antibiotics |
| What is a technique used to amplify DNA, it requires a heat stable protein like Taq polymerase? | PCR, polymerase chain reaction. Cloning is another way to amplify DNA |
| What tpye of sequence would you expect to be a restriction site? | a palindromic sequence. reads same in both directions CATATG GTATAC. |
| What technique uses didoexynucleotides? | Sanger's method of DNA sequencing. requires 4 diferent reactions all using different dideoxy's. |
| Why does DNA migrate to the positive electrode in gel electrophoresis? | DNA is negatively charged, so it migrates to the positive cathode |
| How does RNAi work? | Inhibitory RNA, binds to endogenous RNA and induces degredation of target mRNA. |
| What are recombinant DNA techniques based on? | the fact that there are polymorphisms in the human genome. |
| What can a DNA chip tell you? | what alleles you have, what genes are are expressed, and can predict sensitivity to different drugs. newer technique |
| RFLP's? | restriction fragment length polymorphisms. used to find mutations based on fragment lenghts. |
| In the questions to this assignment DNA sequencing was used on sample of amniotic fluid to determine whether the fetus had the sickle cell mutation. Why couldn't the hemoglobin electrophoresis have been used? | The fetus would have fetal Hb, so the beta globin wouldn't yet be expressed. |
| The case of ADA deficiency which is the cause of some SCID's used a process where "normal" adenosine deamminsae was injected into the patient is an example of? | protein therapy. Proteins are either purified from a source or made recombinantly, (like insulin these days)Recombinant protein drugs are made by introducing a gene to a medium it will grow in, you make a big batch then purify it. expensive. |
| What is another option for getting protein drugs? | using transgenic animals. modify the animal with a gene from another species, ie goats that have been engineered to produce protein drugs in their milk. could cut down the cost. |
| How do antisense drugs work? | they are oligonucleotides with sequences that are complimentary to the RNA you are trying to supress. Blocks translation. poss a antisense drug for hypercholesterolemia in 2012. |
| SiRNA? | SiRNA, small inhibitory RNA and RNAi. prevent expression of target mRNA molecule, but delivery is a problem because of degredation. |
| What is a newer solution people are using to deliver some of these therapeutics? | nanotechnology |
| Gene therapy is similar to protein therapy in concept, you are introducing a normal gene to acheive the desired outcome. what are some possibilities? | direct killing, stimulate immune response, gene augmentation, drug succeptibility genes. |
| How do viral vectors work in gene therapy? | you are using a modified virus to deliver a specific gene to host cells. Cool because you can use the specificity (tropism) of viruses to different cell types to your advantage. These viruses must made to be replication defective, and stay that way. |
| What are some ways to introduce genes into somatic cells in vivo? | injection, gene guns, viral vectors, or vehicles liki liposomes or nanoparticles |
| What is a risk when using retroviruses and transposons? | they will be integrated into the chromosomes so from there on all daughter cells will have the gene, this creates a risk for insertional mutagenisis. Using episomal replication does not carry this same risk because it is "extrachromasomal" |
| What are the most common delivery methods in gene therapy? | Adsenovirus, retrovirus, naked/plasma DNA |
| What are some challenges to gene therapy? | need time to be effective(may require multiple rounds of therapy), immune response may occur, possible that viruses will become replication competent, hard to control where they go, difficulty in treating disorder caused by multiple genetic changes, $$$$ |
| Totipotent and pluripotent stem cells have very similar qualities, what is the difference? | totipotent cell can become anything including extraembryonic. Pluripotent is the gold standard that can differentiate into any cell of the body. |
| What is the restriction of multipotent stem cells? | restricted to making cells from withhin its germ layer, ie mesodermal, ectodermal.. |
| what are 4 ways we get stem cells? | 1. IVF embryos (aborted or miscarried) 2. SCNT=cloning (sheep, goat, cow, pigs...been cloned) 3. Altered nuclear transfer is SCNT modified som it cannot become an embryo. 4.iPS, iPSC=induced pluripotent SC |
| what is cool about iPSC? | taking a somatic cell and through significant manipulation making it a pluripotent stem cell. you are basically rewinding the cells history and it reverts back to an embryonic state. |
| Once you introduce the stem cells the challenge is how to get it to differentiate into what you want, how? | exposure to correct environmental and growth factors, it's not easy. |
| What is the one currently used stem cell pruduct? | using donor marrow (allogenic) for bone fractures. |
| Xeroderma pigmentosa is a cancer caused by the bodies inability to repair? | thymine dimers cause by UV radiation. very sensitive to sunlight. |
| Prokaryotic gene regulation is much simpler than eukaryotic. In prokaryotes the mRNA is polycistronic, so multiple genes code for multiple proteins. transcription and translation are coupled. How is it regulated? | The operon= promoter and structural genes. The operon is controlled by the operator which turns the genes on or off. The operator is controlled by repressor proteins. Inducers will bind repressors to inhibit them. |
| So are the genes on or off when the inducer binds the repressor protein? | Genes are on, the repressor is off allowing the RNA polymerase to bind.... |
| What are longer exons or intron? What has the info? | Introns make up the majority or our DNA but the Exons have the coding material. Introns however make it less likely that all those mutations happening will have serious consequenses. |
| Regulatory sequences are found upstream, how close to they have to be to the promotor region? | They don't have to be close. |
| Heterochromatins and euchromatins regulate genes, how do they work? | Effect how DNA interacts with histones. Heterochromatin=condensed DNA=OFF, it is wound tight around the histones. Euchromatin=decondensed=ON, it is unwound from the histones. |
| HDAC and HAT are 2 proteins control this winding and unwinding of DNA around histones, which does what? | HDAC=OFF(repressor)=removes and acetyl group from histone and it becomes more + charged so it binds tightly to the neg DNA. HAT=ON(initiator)=acetylates the histone making it more neg so it relaxes from the neg DNA. |
| What to transcription factors recruit? | RNA polymerases. Pol II specifically. Pol I os for rRNA and Pol III is for tRNA, snRNA and 5SRNA. |
| What acts as a transcription factor for the synthesis PEP-CK? | glucocorticoids turn it on. |
| Nutshell, transcription factors bind DNA (via 4 binding sites) recruit Pol II and this activates.... | transcription |
| What happens when RNA is not capped? | 5'-3' exonucleases will degrade it. doesn't happen often b/c capping happens quickly |
| What will be around longer, an RNA with a long polyA tail or a short one? | Poly A tails serve to stabilize RNA and the length of the tail correlates to its 1/2 life |
| Splicing out introns is key to translation, why? | Introns have lots of stop codons that cant be translated. if you cant splice them out the RNA is targeted for degredation. |
| Some sequences of the intron are critical ie branch points as well as fascilitating their own removal. How do they do this. | The invariant sequences are important for binding snRNP's. SR proteins bind to slpicing enhancers (ESE's) which recruit the snRNP that splice out intron and ligate the exons. |
| Our example of this was G6PD. In the fed state insulin phosphorylates SR proteins that bind ESE that activate snRNP, splicing occurs and you get protein translation. In the fasted state... | hnRNP binds instead and prevent splicing which =RNA degredation and no protein. |
| Alternative splicing occurs in 75% of our genes, how does it work and what regulates? | Basically take 1 gene and 1 mRNA, splice it into different RNA because you can recombine exons anyway you like. Yields differt RNA's therefore different proteins. snRNP and hnRNP controll this. |
| Some examples of alternative splicing? | diffferent genes that allow for hearing different range of Hz. And the same gene that makes calcitonin also makes the neurotransmitter CGRP. |
| RNA editing is the modification of? | a single nucleotide. Apo B48 and APOb100 are from the same RNA, however a single nucleotide substition makes a stop codon when it is only 48% done. so different message=different protein. This is also how ebola bypasses our immune system. |
| Transcript stability? lots of IRE and IRE BP. The Ferretin(iron storage) and iron and when RNA would or wouldn't be translated. | If you have low iron you have low ferritin (not much to store) , it is not present to bind IRE-BP so IRE-BP will bind with the IRE and the message will be degraded. When the IRE is not bound the message continues. |
| nonsense mediated decay is a normal process, what does it do? | It is when a stop codon is not where it is supposed to be. It function is to chop up messed up RNA so no abberant proteins are synthesized. |
| How can nonsense mediated decay explain Thalessemias? | If the RNA for the alpha globin is decayed you end up with more beta globin. Schmid metaphyseal chodrodysplasia is b/c of a stop codon that targets it for destruction and you get a collagen X deficency. |
| Ligers and Tigons are an example of? | Genetic imprinting. |
| What is the key to genetic imprinting? | the fact that males and females methylate genes differently. |
| Prader Willi and Angleman syndrome are both on chromosome 15 but are very different phenotypically. | Prader Willi when the maternal genes are expressed (2 is methylated) Angelman's is when the paternal genes are expressed (#1 CH3) |
| What do women do via methylation that men don't? | X inactivation |
| Why is methotrexate an effective cancer drug? | inhibits folate from participating in the dUMP reaction so it stops the synthesis of dTMP so slows down DNA replication. |
| What form do you have to activate dietary folate to? | monoglutamate, This is a 2 step reaction, both steps require dihydrofolate reductase. It comes that way in suplements. |
| After folate transfers its carbon how can you recycle it? | 1 way. After the carbon has been transfered folate recycles to accept a new carbon, it does this in its most stable form= N5-methyl FH4 and the carbon of this moiety can be transfered to B12. |
| How do we get dietary B12 if it can only be synthesized by bacteria? | by eating things that ingest bacteria that can make it. meat, eggs, fish. |
| What are the 2 forms that B12 is converted to after we ingest it? | methylcobalamin and deoxyadenosylcobalamin. Cyanocobalamin is the form in most supplements, this fact is important in the Schilling test. |
| B12 absorption and transport requires carriers? | TCI carriers-----bind to IF*****---released---binds TCII---uptake of complex via TCII receptors. liver also uptakes and stores(lots). Intrinsic Factor IF is key. |
| What are the 2 reactions that reqiure B12? | Homocysteine--->Methionine and methylmalonyl CoA--->succinyl CoA. |
| Methylamalonyl CoA --> succinyl CoA requires? | adenosyl B12. diagnostically you would see a build up of methylamalonic acid if not enough B12. So high methylmalonic acid=B12 deficiency |
| B12 is also required for the renethylation of of homocysteine to methionine. (so is SAM and Folate) | to get folate to N5-methyl-FH4 you use MTHFR. From here N5-methyl-FH4 gives carbon to B12. B12 gives to methionine and SAM gets it in the way down to homocysteine. This makes more sense in a picture. |
| So if you are deficient B12, folate, MTHFR, or B6 (PLP) your homocysteine levels would go up because the renethylation path is shut down. What about too much SAM ie from supplements? | This too would increase the amount of homocysteine. |
| What ot her reactions is SAM involved in? | making creatine, methylated nucleotides, melatonin. Popular dietary supplement, atheletes for creatine, others for depression. Jury is out on whether it works. |
| Homocysteinemia = elevated levels in blood. It can cause infertility miscarriages, neuro disorders, cancer, and it is linked to Cardiovascular Disease. What are the symptoms when you have a mild homocysteinemia? | very common and generally asymptomatic however it increases your risk for all of the above, and there is a possible link to obesity. Treat with B12 and folate supplemets |
| Macrocytic anemia, your RBC's larger and fewer of them. Think? | B12 and Folate. Sypmtoms. loss of appetite, tingling in extremeties, pale skin, tired, diarrhea. Neuro also w B12. |
| How is B12 and Folate connected to macrocytic anemia? | Methyl trap. you wind up with a functional folate deficiency (no dTMP) because you need folate to get methycobalamin and you need B12 to recycle folate (the N5-methyl FH4 form). So no B12 = no recycling and the N5 -methyl-FH4 builds up. |
| A few causes of B12 and Folate deficienies. | dietary lack, chronic alcoholism, abdominalk surgey, GI disease, pernisciou anemia (no IF) |
| What do you look at to diagnose these deficiencies? | serum B12 and folate, MCV (mean corpuscle volume), ,homocysteine and methylamalonic acid levels, Schilling test |
| Elderly peopl are more likely to have a B12 deficinecy due to gastric atrophy. (messes up pH and IF). This is bad because it could be misdiagnosed for? | dementia, because the neuro effects the deficiency is having. A lot of docs automaticaly give elderly B12 shots, wont hurt if they dont need it. |
| What is Epigenetics? | HERITABLE phenotype resulting from changes in a chromosome WITHOUT alterations in DNA sequence. It is the link between environment and gene expression. |
| It's all about DNA methylation. | A mom with a low carb diet has increased DNA methylation which can increase the childs tendency for obesity. |
| How can this explain why even a very well controlled diabetic still has a higher risk for kidney disease? | Metabolic Memory Hypothesis. cells having a "memory" from transferred methylation patterns. |
| Some anticancer drugs are targeting DNA methyltransferases. | methylation is also involved in silencing retrotransposons. |
| Pyrimidines and Purines, what is what? | pyrimidines=1 ring=C U T. purines=2 rings=A G G and C pair. A and U or A and T(DNA pair |
| In polymerization nucleic acids are joined by a phosphodiester bond (triphospahte bonds supply the energy). Which end are you adding to? | 3' DING. always 5' to 3' |
| Why is DNA in a double helix? | one reason is so RNAases don't destroy it, same reason DNA is deoxy. |
| What is the most common form of the DNA helix? | Beta, 10 bp's per turn. Major groove and minor groove. Major groove provides more access so it's normally where regualtory proteins bind. |
| What amino acids are Histones rich in that allows them to bind to the neg DNA? | Lysine and Arginine |
| Nucleosomes are? | histone octamers and assciciated DNA, form Left handed super helix. Solenoids are nucleosomes that coil around each other to form hollow tubes, and solenoid tangling is involved in forming the mitotic or meiotic chromosomes |
| Scaffold proteins bind DNA tighter than histones, they serve to? | tie solenoids together and they maintain supercoiling. topoisomerase II is one |
| What is a karyotype? | number, size and banding patterns of all mitotic chromosomes |
| How many genes do we have? | ~31,000. only 5% encode protein, and only 1/3 are transcribed into RNA |
| All the rare sequences combined comprise 1/2 our genome. | most functional genes belong to this class. they take the longest to reanneal because the sequence is so rare. |
| Most intermediate sequences are? | retrotransposons. Transposons are "jumping genes" that can move around in the genome. Retroviruses are parasitic DNA molecules that can move from cell to cell without the use of an RNA intermediate |
| So what are retrotransposons? | 45% degenerate(mutations have caused them to loose their ability to jump) so they typically don't cause problems. Alu sequences are a rare exception |
| Your "house keeping" genes belong to a Functional intermediate class. Some of these are? | rRNA, 5S RNA, tRNA and histones |
| gene families are groups of genes with similar sequences | OTC and PEP carboxykinase in same family |
| If 2 genes have a similar sequence, they probably evolved from a single ancestor. | homlogy, ie 80% homologous = 80% of sequence is identical |
| regions where sequences remain similar, prob because they are important for function, are called? | conserved domains |
| What do you need for DNA replication?> | DNA polymerase, Mg, template, dNTP's, Primer |
| What does the proofreading? | 5'-3' exonuclease, it removes mismatched nucleotides. Pol delta and gamma check it out, the exonuclease does the excision. |
| DNA replication is discontinuous, why? | Leading strand synth in correct 5'-3' direction but lagging strand cant be b/c going the other direction. Solved by looping the strand so Okizaki fragments can be syth in the proper direction |
| Semiconserevative means? | 1 strand is de novo the other is inherited intact from a parental chromosome. |
| what does helicase do? | unwinds DNA opening the double helix so DNA polymerase can replicate the strand. SSB's stabilize the single strands so it wont wind back up into helix |
| the beta clamp is part of the DNA Replication apparatus, what does it do? | allows for longer strands. Helicase, DNA polymerase and Pol a and primase are also part of this apparatus |
| How do you remove primers from the lagging strand? | RNAase removes the primer by digesting any primer. DNA polymerase B fills in the gaps left by the RNAase, and DNA ligase binds any free 3' to 5' prime and seals the "nicks" left by Pol B. |
| When helicase unwinds the DNA it affects the supercoiling, what adjusts this? | topoisomerase. |
| How do you deal with the overhang left behind by the lagging strand? | Telomerase. it is a reverse transcriptase so it uses RNA as a template for DNA. this extends the length of the telomeres and protects them, BUT also involved with cnacer and immortality of cancer cells. Telomerase activity decreases with age. |
| Promoters are regions used to activate or repress trnascription of a gene, they cannot be moved. How are enhancers different? | Enhancers regulate like a promoter, but they can be moved relative to the gene its regulating and the 5'-3' orientation can be flipped |
| promoters and enhancers are actually recognition sequences that are bound to transcription factors. what are the 2 most common? | TATA box and CCAAT box. Most minimal promoters for Pol II have the TATA sequence |
| Transcription factors have 2 domains, a binding domain and an activation domain. What happens when there is only a binding domain? | The activation domain induces RNA synthesis by recruiting RNA polymerase, so if there is no activation domain the transcription factor acts as an inhibitor of transcription |
| What are the 4 transcription factor families? | hleix turn helix; zinc fingers; helix loop helix; Leucine zippers. |
| helix turn helix? | think hox genes, binds DNA by wedging into major groove. zinc fingers also wedge into major groove, but are weaker so you need more of them |
| helix loop helix? | form heterodimers, 2 diff polypeptides must bind before they will bind DNA. Leucine zippers, also form dimers, are held together in a helix with their hydrophobic faces out, they form the scissor grip on DNA |
| What is the first thing you need to do to translate protein? | assemble some ribosomes. rRNA makes up ~90% of our total RNA, (functional intermediate) |
| Where in the cell are ribosomes produced? | Nucleolus, region of the nucleus, this is NOT a membrane bound organelle even though it may look like one..DING. it looks like this because so many ribosomes are pouring out of it. |
| Oscar Miller Feathers? | way to elevate rRNA abundance. each gene can simultaneously produce multiple transcripts |
| rRNA is polycistronic. | each gene codes for three rRNA's via Pol I. rRNA does the translating, but it is not translated itself. |
| What do riboncleoproteins do? | assemble around the rRNA to form the large and small subunitsof ribosomes. |
| now you have tRNA, it undergoes extensive post translational modofication. what is one very important modification? | anitcodon loops (folding into clover leafs). these anticodons are complimentary to a specific mRNA codons, the anticodons will bind the codons and this is how they specify amino acids. |
| You now have all the machinery to make protein, but how do get it out of the nucleus so translation can occur? | huge, nuclear pore complexes usung inportins and exportins. |
| once tRNA get to the cytoplasm there is one more thing you have to do before translation? | tRNA charging, it requires ATP. you have to bind the 3' group of the tRNA with the carboxyl group of the amino acid specific to that tRNA. |
| how do 4 nucleotides code for 20 amino acids? | every 3 bases in mRNA codes for a different amino acid. then you run all the possibilties of those combinatiions and you get 64 possibilities=multiple codos code for the same amino acid. |
| When this happens where do you usually see the change in the codon? | the 3rd base. it is called wobble and is another feature that lets us escape from some mutations. |
| What is the start codon? | methionine codon, AUG. all have to start with AUG, but what if you dont need a methionine in your protein? you cleave the amino terminus to remove it. |
| translation will continue until it hits one of 3 stop codons, they are? | UAG, UGA, UAA |
| P sites and A sites... | P site is region of ribosome that binds tRNA tha tis attahced to the growing polypeptide. A site region of ribosome that binds the aminoacyl tRNA for the next amino acid to be bound to the growing polypeptide. |
| What is important to remember about this? | that the polypeptide is actually added to the AA, not vice versa. |
| Once the protein is made it needs to be sorted, where does this happen? | a region of the protein called the signal sequence is bound by a docking protein, which in turn binds a receptor (eg transmembrane type III) on the organelles membrane allowing the protein to be translocated through a channel in the membrane. |
| more on sorting...from the rough ER proteins have to get to their final destination, plasma membrane, lysosome, or extracellular secretion. How does this happen. | refered to as intracellular membrane trafficking, from the ER through the cisternae of the golgi towards the plasma membrane, futher sorted as they go. E face=lumenal sideo of organelles and vesicle. P side=cytoplasmic side. |
| Difference between mutations and teratogens? | a mutation is any change in DNA sequence, NOT a congnital defect, though one may result from a mutation. DING. Teratogens are factors that interfere with developmental processes without changing DNA, they will NOT be heritable, ie fetal alcohol synd. |
| What are some reasons that mutations are silent? | 2/3 of our DNA is intron, wobble, spacer regions, could make a similar AA that may not effect finction, could effect a part that does not code for a critical part of the protein, like linker regions |
| point mutations. transition mutation=sub a purine for purine or pyrimidine for pyrimidine. a transversion mutation is when you sub a purine for a pyrimidine or vice versa. 3 point mutations are? | Missense=a single bp substitution altering 1 amino acid. Nonsense mutation=a bp substitution producing a premature stop codon (truncated protein). Frameshift= insertion or deletion of a sequence, not in a multiple of 3=random sequence after the change |
| chromosomal abberations are deletions, insertions, or duplications. What criteria has to be met before something is called a chromosomal abberation? | must be visible under light microscopy. |
| What is the most important thing to do if you have a child affected with chromosomal abnormality? | cytogenetic analysis of the parents |
| a translocation is a? | misplacement of a DNA fragment to a different location in the genome. |
| what happens when you have recipricol translocations? | you get a scenarion where carriers can be unaffected, but some of their children may be. in a duplication deletion you get 3 copies of 1 and 1 copy of the other, this messes up gene balance=problems. eg chromosome 3 duplication deletion syndrome |
| What kind of chromosomal abberation is involved in cri-du-chat? | a deletion of part of the short arm of chromosome 5 |
| one is an effect triploidy can have on an expecting mother? | some triploidies can develop into hydratidiform moles that develop with little fetal tissue and vascualture so fluids do not drain form placenta. villi become swollen "bunch of grapes" and cen develope into malignacy= choriocarcinoma. 20% mortality |
| Aneuploidy? older women have a greater chance of this occuring. | wrong number of 1 chromosome in a parental set. trisomy, monosomy. causedd by a nondisjunction which is a failure of the chromatids to seperate during meiotic anaphase. |
| trisomy 21? survival of aneuploidies is more likely when they affect the shorter chromosomes. | downs syndrome. 90% spontaneously aborted. |
| trisomy 18 is Edwards syndrome. DING. why? | unmisatkeable presentation of clenched fists with the 2nd digit overlapping the 3rd and the 5th digit overlapping the 4th. rocker bottom foot, fawn like ears, profound mental reatardation, stay babies their whole lives. not many survive. |
| Patal syndrome is a trisomy of what chromosome? | trisomy 13. >95% spontaneously abort. prominent proboscis, holoprosencephaly, cleft palalte. |
| Turner syndrome is a monosomy (XO). what are symptoms? | female with no ovaries, limited 2nd sexual characterisitic, low ears, webbed neck(from cystic hydromas), broad shield chest, no mental retardation |
| an extra X chromosome (XXY) where males have female 2nd sex characteristics, gynomatia, small testes, little body hair. Normal IQ's, usally tall, sterile? | Klinefelters. |
| What do you see phenotypically on someone with an extra sex chromosome (XXX, XYY)? | very little, slightlt reduced IQ, learning disabilities, ADD,ADHD = increased incidence in prison populations |
| What causes inversions, translocations and deletions? | DNA ligase errors. DNA ligase will join any free 3' with any free 5' but may not join them in the correct sequence. |
| mistakes in proofreading? | DNA polymerase infidelity |
| How does the cytochrome p-450 system cause mutagenisis? | cyt p-450 is a natural process occuring in liver that function is the removal of toxins. It oxidizes hydrophobic compounds to make them more soluble so they can be excreted. However somtimes this turns innocuous products into mutagens |
| Depurination, deamination and tautomeric shift are all spontaneous. Problems arise when this occurs during replication because it stabilizes the mutation. | tautomeric shifts will casue transversion and transition mutations. |
| There 3 types of radioactivity that can affect our genes? | UV light=thymine dimers, weroderma pigmentosum. Ionizing radiation=point mutations. Gamma rays=induces chromosomal abnormalities, can penetrate tissues, think gonads and your F2. |
| Some chemical mutagens? | Alkylating agents (mustard gas)=point mutations and chromo abnormalities. Strand cleavers=peroxides, sulfer compounds, gamma rays. Base analogs (bromouracil) mimic nucleotides, get tautomeric shifts. |
| 2 more chemical mutagens | intercalating agents (agent orange) wedge between bases and can break strans esp during replication b/c increased stress. Insertional elements= viruses and transposons, jump around and either add or delete as they do this. |
| With all that can go wrong, what are some ways to repair problems? | proofreading, DNA ligase, dorect base repair, excision repair. Excision repair is like what happens in replication with the lagging strand. 3'-5' exonuclease removes section, DNA Pol B fills the gaps, and DNA ligase smooths out the nicks. |
| Is facilited diffusion passive or active? | passive, the difference b/w it and passive diffusion is that facilitated has to go through specific transmembrane proteins. more specific and faster, but are saturable b/c limited number of channels |
| Active transport requires energy, usually from what? | ATP, the energy allows movement against a concetration gradient of electric potential. This is done with ATPase pumps |
| there are 4 classes of ATPase pumps, what makes up the majority? | P class ATPases. phosphorylated, ion pumps, ie Na/K ATPases. F class are the ones involved in the mitochondria , they are opposite of most pumps b/c they are going down the gradient to MAKE ATP(ox phos). V class = lysosomes, used to lower pH |
| MDR-1 is an ATPase pump that excretes hydrophobic compound from tissues and so serves to detoxify cells. How can this pump be realted to cancer? | many cancer drugs are hydrophobis, so the pump spits them out too. Esp bad when mutations in cancer cells cause an overexpression of the pump. ie became more resistant to the cancer drug |
| CFTR functions as a channel (ATP is required to open the channel) It allows for movment of Na and Cl ions into the mucus lining the airways of the lung. | Through osmosis the ions draw in water to thin out the mucus. people with CF the CFTR isn't working. Lung is not the only tissue this is found in and accounts for the secondary symptoms assoc. with CF salty sweat,male sterility, pancreatic hytpoglycemia |
| What is a good example of a coupled system? | H+/K+ ATPase. secretes HCl into the lumen of the stomach and bicarb out the other side into the blood, which is also where it is getting the Cl- for the HCl. |
| receptors and ligands? | receptors are cellular factors that bind a specific ligand to induce a response. Ligands are molecules that are bound by other molecules like receptors. |
| Hormones control metabolism or physiology. Growth factors control cell cycle progression, cellular differentiation or cell morphogenisis during development. What do cytokines do? | growth factor involved woth hematopoiesis |
| hydrophilic ligands, like insulin, epi, and histamine cannot traverse membrane so they bind to transmembrane receptors, but they can travel freely in the blood. They are rapid response with short half life-rapidly cleared (seconds to minutes) | Hydrophobic ligands, steroids and FA's, require binding proteins to travel in te blood, but can cross membranes to bind intracellular receptors. Hard to store so you make them as you need them. Slow response, longer half life. (hours to days) |
| Some receptor characteristics.. | high specificity, low Km, saturable, reversible binding, tissue specific distribution, biological response |
| Nuclear receptors (steroid receptors) bind hydrophobic ligands. Steroids usually. What are 3 subfamilies? | glucocorticoids, estrogen, non steroid(thyroid hormones and retinoic acid receptors) They also serve as zinc fingers. |
| Transmembrane receptors are required for hydrophilic ligands to cross into cell. what are the 3 domains? | extracellular ligand binding domain, transmembrane domain, and signal transduction domain |
| Some examples of receptors and their signaling pathways... | 7 transmembrane receptors=cAMP and phosphoinositide. tyrsine kinase=RAS. serine/threonine kinases=TGF beta |
| In TGF beta signaling what ultinmately controls whether gene transcription is activated or inhibited? | The heteromeric Smad complex (Smads and coSmads) translocate to the nucleus where they act as a transcription factor |
| Ras-MAPK. If I was a biochemist i might call it "elegant" GEF plucks GDP off Ras, Ras refills with GTP (lots around) Ras is activated by GTP in turn it activates RAF which phosphorylates MEK which phosphorylates MAP kinsae. what does MAP kinsase do? | it is badass. it goes on to phosphorylate enzymes, transcription factors and MAP's. but it does this exponentially. every kinase molecule goes on to phosphorylate hundres of others. ACTIVATION CASCADE=huge response from tiny signal. |
| What inactivates the Ras-MAPK pathway? | phosphatases and GAP's always there but the activation signal is stronger when it's running |
| what activates cAMP pathway? | G coupled proteins. the receptors are 7 transmembrane receptors(7 alpha helices). Ras and G alpha are homologous |
| G alpha does all the work, the others G's really serve to sequester the G alpha. G alpha binds to adenylate cyclase which converts ATP to cAMP, DING, it is a second messenger. Then... | cAMP activates protein kinsae A (PKA) which then phosphorylates the proteins. this can be turned off by cAMP phosphodiesterase by converting cAMP to AMP. (PKA was also involved in CFTR, and glucagon/cortisol) |
| Where does the cholera toxin affect the cAMP pathway? | inhibits the GAP domain of G alpha. leads to massive diarrhea and death due to dehydration. |
| Phosphoinositide signaling. PLC cleaves PIP2 into IP3 and DAG (2 routes). the short route PKC binds DAG, DAG activates the kinase activity if DAG and it effects downstream. the longer way.... | the IP3 goes to ER or endosomes binds and opens Ca channels (Ca as 2nd messenger) Ca does lots, muscle contraction, but also is the cross talk b/w paths. Ca stimulates the phosphodiesterase that shuts off cAMP |
| However to finish the path. | Ca also targets PKC which as with the short route, PKC binds DAG is activated and acts on downstream substrates. |
| 2 clinical correlations of the phosphoinsitide signaling path. one is that the pertussis toxin blocks PLC activation leads to whooping cough. the second? | Lithium. |
| I did not get to.... | differntiation |
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