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67 Cards in this Set
- Front
- Back
Chronic myelogenous leukemia: how does this happen? How is it diagnosed and treated? |
Translocation at chr9/chr11 with chr22 (Philadelphia chromosome); FISH/CISH, treated with tyrosine kinasr inhibitors |
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EWINGS sarcoma: how does this happen? How is this diagnosed? |
Translocation between chr11 and chr 12; qPCR, yields product only if translocation is present |
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Acute lymphoblastic leukemia: how does this happen? How is this diagnosed? |
Translocation between chr12 and chr21; FISH/CISH/qPCR |
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Follicular lymphoma: how does this happen? How is it diagnosed? |
t(14;18); FISH/qPCR |
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Promyelocytic lymphoma: how does this happen? How is this diagnosed? |
t(15;17)(q22;12); FISH/qPCR |
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Mantle cell lymphoma: how does this happen? How is this diagnosed? |
t(11;14)(q13;q32); FISH/PCR/qPCR |
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Burkitt lymphoma: how does this happen? How is it diagnosed? |
t(8;14)(q24;q32); FISH/CISH |
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Rhabdomyosarcoma: how does this happen? How is it diagnosed? |
t(2;13)/t(1;13); qPCR/PCR/FISH |
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HER2/neu breast cancer: how does this happen? How is it diagnosed? |
Over expression of HER2; IHC/FISH/CISH |
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Why does a mutation to tp53 cause cancer? How is it diagnosed? |
Tp53 codes for p53 which helps arrest mitosis. When tp53 is mutated between exons 4-9 or exons 5-8, p53 is unable to arrest cell cycle causing continual proliferation of cells; Single strand conformation polymorphism/sequncng/FISH |
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BRCA1/2 regulate what kind of proteins? Where are these genes located (chromosome)? What kind of cancer is associated with mutations to these genes? |
DNA repair mechanism; located at chr17/13; Breast cancer |
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Alpha thalassemia is associated with what disorder? What genes are associated with the alpha thalassemia? What effects are associated with alpha thalassemia? |
Hemoglinopathy; HBA1 and HBA2 on chr16; decreased alpha-globin resulting in excess beta (adults) / gamma (newborns) chains which cause the formation of unstable tetramers leading to abnormal oxygen dissociation curves |
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Prader Willi Syndrome is caused by what? |
genes on chr15 of the paternal side are deteled, causing the maternal's chr15 to be silenced through epigenetics |
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Angelman syndrome is cause by what? |
genes on chr15 of the maternal side are deleted, causing the genes on paternal chr15 to be silenced through epigenetics |
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Beta thalassemia is associated with disease? What is the cause of beta thalassemia? |
Hemoglinopathy; mutations to the HBB gene (chr11), severity of the mutation(s) dictates the severity of the condition |
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Prothrombin is aka ________; If there are mutations to the ________ region of this gene can cause __________ |
Factor II; 3'; the inability to produce thrombin (clotting factor) |
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Ataxia telangiectasia is caused by mutations to what gene? What is the function of the protein? Why is it dangerous? |
ATM; ATM codes for a serine/threonine kinase that phosphorylates key proteins that signal for cell cycle checkpoints/DNA repair/apoptosis; if ATM is mutated cell cycle arrest cannot be signaled due to double stranded breaks made during mitosis |
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What is EGFR? What chromosome is it mapped? |
Epidermal Growth Factor Receptor; chr7
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What is the most common cause for cystic fibrosis? What happens in people with cystic fibrosis? |
3 bp deletion (deltaF508) to the CFTR (cystic fibrosis transmembrane conductance regulator) gene; CFTR protein is a transmembrane pump that is continually closed |
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Hemochromatosis is caused by what? What happens with this disorder? |
HFE gene mutation causes cells inability to recognize iron storage in heme groups causing the body to continually absorb iron from blood
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Stringency: removing Mg2+ ions from PCR mix |
Increases stringency; used to optimize amplification; too low concentration no product; too high mispriming increases and non-target DNA is over amplified |
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Stringency: Increase Temperature |
Increases stringency; only primers with high percentage of complement bases will be able to bind at higher temps |
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Stringency: increase probe length |
Increase stringency; higher specificity for target region of DNA |
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Stringency: increase PCR probe complexity |
Increase stringency; GC richness and consecutive nucleotide repeats greatly affect the specificity and Tm for probes |
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Stringency: higher salt concentrations |
Lowers stringency; shorter PCR fragments will be able to disassociate from template strand preferentially to longer fragments |
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Stringency: less time |
Increases stringency; shortens the amount of time for mispriming to occur |
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What some PCR inhibitors? |
Hemoglobin; heparin; xylene; phenol; cyanol; bromophenal blue |
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Preferred tubes for collecting blood specimen for PCR assays? What would be a bad tube? |
Lavendar (EDTA) and Yellow (ACD = acid citrate dextrose); Green (Heparin) |
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Function and Eukaryotic/Prokaryotic: DNA polymerase alpha |
Lagging strand synthesis during DNA replication; Eukaryotic |
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Function and Eukaryotic/Prokaryotic: DNA polymerase beta |
DNA repair mechanisms and replication restart at nicks and lesions; Eukaryotic |
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Function and Eukaryotic/Prokaryotic: DNA polymerase delta |
leading strand synthesis; Eukaryotic |
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Function and Eukaryotic/Prokaryotic: DNA polyermase epsilon |
mostly repair for polyermase delta errors, minor role in replication; eukaryotic |
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Function and Eukaryotic/Prokaryotic: DNA polyermase gamma |
mitochondrial DNA replication only; eukaryotic |
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Function and Eukaryotic/Prokaryotic: DNA polyermase 1(Pol I) |
lagging strand synthesis, 16-20 bases/sec; p-rokaryotic |
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Function and Eukaryotic/Prokaryotic: DNA polyermase 2 (Pol II) |
DNA repair mechanisms and replication restart at nicks and lesions, 40 bases/sec; prokaryotic |
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Function and Eukaryotic/Prokaryotic: DNA polyermase 3 (Pol III) |
leading strand synthesis, 250-1000 bases/sec; prokaryotic |
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Function: RNA polymerase 1 (RNA Pol I) |
rRNA synthesis |
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Function: RNA polymerase 2 (RNA Pol II) |
mRNA synthesis |
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Function: RNA polymerase 3 (RNA Pol III) |
tRNA and snRNA synthesis |
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Function: Type 1 Restriction Enzyme |
recognition site is comprised of two specific portions one containing 3-4 bp, the other 4-5 bp spaced out by 6-8 bp; cleaves DNA at least 1000 bp from recognition site (restriction activity); HsdM subunit is capable of methyltransferase activity |
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Function: Type 2 Restriction Enzyme |
recognition sites are palindromic sequences; breaks are made near or at the recognition site leaving "blunt" or "sticky" ends |
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Function: Type 3 Restriction Enzyme |
recognition site is comprised of two nonpalindromic sequences; restriction activity occurs 20-30 bp from recognition site |
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Function Type 4 Restriction Enzyme |
target methylated DNA, including hydroxymethylated and glucosyl-hydroxymethylated bases; cuts 10 bp, 3' end from restriction site |
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What is the difference between DNA and RNA bases? |
2' carbon has -H in DNA, where RNA has -OH |
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Draw adenine:thymine hydrogen bond (chemical structure) |
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Draw guanine:cytosine hydrogen bond (chemical structure) |
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Describe the following mutations: 1) substitution, 2) deletion, 3) insertion, 4) frameshift |
1) single base is switched with another 2) base(s) are lost (deleted) from sequence 3) extra base(s) are inserted into sequence 4) typically a result of one of the aforementioned mutations, causes codons to be parsed and read differently |
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What is the ori? |
origin of DNA replication |
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Function: helicase |
unwinds DNA and stabilizes replication with aid from SSB (single-strand binding) proteins |
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Function: primase |
primes lagging strand synthesis by laying down short RNA complement strands
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Function: gyrase |
relieves strain induced by helicase by relaxing DNA from super-coiled conformation
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List and describe steps of transcription in eukaryotes |
1) pre-initiation - transcription factors (TATA-binding protein) bind to promoter region (TATA box, found -30. -75, -90 from coding region) and recruit RNA polymerase (NOT BOUND TO DNA), activators and repressors 2) initiation - once all necessary transcription factors have assembled RNA polymerase binds to DNA 3) promoter clearance - RNA polymerase clears promoter region by several rounds of abortive initiation (produces truncated RNA transcripts) 4) elongation - RNA polymerase uses the template strand to produce a synonymous RNA sequence of the coding strand; multiple RNA polymerases can be recruited to produce many RNA molecules from a single RNA origin of transcription
5) termination - cleavage of the new RNA transcripts followed by template-independent 3' polyadenylation |
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What is the difference between Rho-dependent and Rho-independent termination in prokaryotic transcription? |
Rho-dependent - protein factor (Rho) destabilizes the template:RNA interaction releasing the RNA molecule from elongation complex Rho-independent - (AKA intrinsic termination) when the RNA molecule forms a GC-rich haripin loop followed by a stretch of uracils, the hairpin destabilizes the template:RNA interaction and pulls the poly-U tail from the RNA polymerase |
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How is mRNA splicing performed? |
Proteins and snRNPs (small nuclear ribonucleic particles) form a complex known as a spliceosome around the intronic regions of mRNA, excising the intron and ligating the exons |
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What is the Shine-Dalgarno box? Kozak box? |
Shine-Dalgarno box refers to the 5' UTR of prokaryotic RNA transcripts Kozak is the eukaryotic version |
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Describe the mRNA:ribosome interaction during translation |
the small subunit (30S) binds to the UTR of the mRNA; traveling along until it comes to AUG codon, then recruits the large subunit (50S) and the tRNA anticodon; the 70S ribosome continues processing the mRNA by housing codon:anticodon sequences in the A site, lengthening the amino acid chain in the P site, and ejecting "empty" tRNA molecules from the E site |
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What are the three stops codon? |
UGA, UAA, UAG |
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What is metaphase? |
stage of cell mitosis where chromosomes are condensed and align along the metaphase plate |
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What makes up the structure of a nucleosome? |
DNA and octameric complex of histones, DNA is wrapped around the complex 2-3 times |
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What is the difference between exonuclease and endonuclease activity? |
Endonucleases are able to cleave the phosphodiester bond in the middle of sequences Exonucleases must start from either 5'/3' end |
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How sensitive is PAGE? |
can differentiate 1 bp difference across lanes |
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What is PFGE best at resolving? |
very large DNA fragments (>50 kbp) |
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What is capillary electrophoresis? |
used for seperation of chemicals and multicompound molecules; samples are dissolved in buffer, the solution then travels through through a glass capillary tube, smaller negatively charged objects travel through faster the larger positively charged ones. These objects are observed passing through the capillary via a fluorescent light and individual objects are measured via absorbance |
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Outline the target, probe and purpose of the following: 1) Southern blot 2) Northern blot 3) Eastern blot 4) Western blot 5) Southwestern blot |
1) DNA, nucleic acid, gene structure 2) RNA, nucleic acid, transcript structure/processing/gene expression 3) Protein, protein, modification of Western using enzymatic detection 4) Protein, protein, protein processing/gene expression 5) Protein, DNA, DNA binding proteins/gene regulation |
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Outline the steps taken to perform Southern Blot |
1) digest DNA w/ restriction enzymes, run on agarose gel, denature DNA using NaOH 2) transfer DNA to membrane using absorption/vacuum/electrohpetic systems 3) incubate membrane with ssDNA probe (radioactive or enzyme-linked) 4) enzyme-labeled probe - incubate with substrate to expose colormetric change; radiolabeled - expose on xray-film |
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What does branched DNA amplification target? How does it work? |
RNA; target RNA is anchored using capture probes, label probes also bind to target, label probes bind to amplifier probes which are then labeled with alkaline-phosphatase oligonucleotides providing signal (2nd gen bDNA binds preamplifiers to label probes followed by amplifiers)
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What does NASBA mean? What does it target? How does it work? |
Nucleic Acid Sequence Based Amplification; |