Ascp Molecular Biology

Front 1

Chronic myelogenous leukemia: how does this happen? How is it diagnosed and treated?

Back 1

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?

Back 2

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?

Back 3

Translocation between chr12 and chr21; FISH/CISH/qPCR

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Follicular lymphoma: how does this happen? How is it diagnosed?

Back 4

t(14;18); FISH/qPCR

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Promyelocytic lymphoma: how does this happen? How is this diagnosed?

Back 5

t(15;17)(q22;12); FISH/qPCR

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Mantle cell lymphoma: how does this happen? How is this diagnosed?

Back 6

t(11;14)(q13;q32); FISH/PCR/qPCR

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Burkitt lymphoma: how does this happen? How is it diagnosed?

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t(8;14)(q24;q32); FISH/CISH

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Rhabdomyosarcoma: how does this happen? How is it diagnosed?

Back 8

t(2;13)/t(1;13); qPCR/PCR/FISH

Front 9

HER2/neu breast cancer: how does this happen? How is it diagnosed?

Back 9

Over expression of HER2; IHC/FISH/CISH

Front 10

Why does a mutation to tp53 cause cancer? How is it diagnosed?

Back 10

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

Front 11

BRCA1/2 regulate what kind of proteins? Where are these genes located (chromosome)? What kind of cancer is associated with mutations to these genes?

Back 11

DNA repair mechanism; located at chr17/13; Breast cancer

Front 12

Alpha thalassemia is associated with what disorder? What genes are associated with the alpha thalassemia? What effects are associated with alpha thalassemia?

Back 12

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

Front 13

Prader Willi Syndrome is caused by what?

Back 13

genes on chr15 of the paternal side are deteled, causing the maternal's chr15 to be silenced through epigenetics

Front 14

Angelman syndrome is cause by what?

Back 14

genes on chr15 of the maternal side are deleted, causing the genes on paternal chr15 to be silenced through epigenetics

Front 15

Beta thalassemia is associated with disease? What is the cause of beta thalassemia?

Back 15

Hemoglinopathy; mutations to the HBB gene (chr11), severity of the mutation(s) dictates the severity of the condition

Front 16

Prothrombin is aka ________; If there are mutations to the ________ region of this gene can cause __________

Back 16

Factor II; 3'; the inability to produce thrombin (clotting factor)

Front 17

Ataxia telangiectasia is caused by mutations to what gene? What is the function of the protein? Why is it dangerous?

Back 17

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

Front 18

What is EGFR? What chromosome is it mapped?

Back 18

Epidermal Growth Factor Receptor; chr7

Front 19

What is the most common cause for cystic fibrosis? What happens in people with cystic fibrosis?

Back 19

3 bp deletion (deltaF508) to the CFTR (cystic fibrosis transmembrane conductance regulator) gene; CFTR protein is a transmembrane pump that is continually closed

Front 20

Hemochromatosis is caused by what? What happens with this disorder?

Back 20

HFE gene mutation causes cells inability to recognize iron storage in heme groups causing the body to continually absorb iron from blood

Front 21

Stringency: removing Mg2+ ions from PCR mix

Back 21

Increases stringency; used to optimize amplification; too low concentration no product; too high mispriming increases and non-target DNA is over amplified

Front 22

Stringency: Increase Temperature

Back 22

Increases stringency; only primers with high percentage of complement bases will be able to bind at higher temps

Front 23

Stringency: increase probe length

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Increase stringency; higher specificity for target region of DNA

Front 24

Stringency: increase PCR probe complexity

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Increase stringency; GC richness and consecutive nucleotide repeats greatly affect the specificity and Tm for probes

Front 25

Stringency: higher salt concentrations

Back 25

Lowers stringency; shorter PCR fragments will be able to disassociate from template strand preferentially to longer fragments

Front 26

Stringency: less time

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Increases stringency; shortens the amount of time for mispriming to occur

Front 27

What some PCR inhibitors?

Back 27

Hemoglobin; heparin; xylene; phenol; cyanol; bromophenal blue

Front 28

Preferred tubes for collecting blood specimen for PCR assays? What would be a bad tube?

Back 28

Lavendar (EDTA) and Yellow (ACD = acid citrate dextrose); Green (Heparin)

Front 29

Function and Eukaryotic/Prokaryotic: DNA polymerase alpha

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Lagging strand synthesis during DNA replication; Eukaryotic

Front 30

Function and Eukaryotic/Prokaryotic: DNA polymerase beta

Back 30

DNA repair mechanisms and replication restart at nicks and lesions; Eukaryotic

Front 31

Function and Eukaryotic/Prokaryotic: DNA polymerase delta

Back 31

leading strand synthesis; Eukaryotic

Front 32

Function and Eukaryotic/Prokaryotic: DNA polyermase epsilon

Back 32

mostly repair for polyermase delta errors, minor role in replication; eukaryotic

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Function and Eukaryotic/Prokaryotic: DNA polyermase gamma

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mitochondrial DNA replication only; eukaryotic

Front 34

Function and Eukaryotic/Prokaryotic: DNA polyermase 1(Pol I)

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lagging strand synthesis, 16-20 bases/sec; p-rokaryotic

Front 35

Function and Eukaryotic/Prokaryotic: DNA polyermase 2 (Pol II)

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DNA repair mechanisms and replication restart at nicks and lesions, 40 bases/sec; prokaryotic

Front 36

Function and Eukaryotic/Prokaryotic: DNA polyermase 3 (Pol III)

Back 36

leading strand synthesis, 250-1000 bases/sec; prokaryotic

Front 37

Function: RNA polymerase 1 (RNA Pol I)

Back 37

rRNA synthesis

Front 38

Function: RNA polymerase 2 (RNA Pol II)

Back 38

mRNA synthesis

Front 39

Function: RNA polymerase 3 (RNA Pol III)

Back 39

tRNA and snRNA synthesis

Front 40

Function: Type 1 Restriction Enzyme

Back 40

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

Front 41

Function: Type 2 Restriction Enzyme

Back 41

recognition sites are palindromic sequences; breaks are made near or at the recognition site leaving "blunt" or "sticky" ends

Front 42

Function: Type 3 Restriction Enzyme

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recognition site is comprised of two nonpalindromic sequences; restriction activity occurs 20-30 bp from recognition site

Front 43

Function Type 4 Restriction Enzyme

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target methylated DNA, including hydroxymethylated and glucosyl-hydroxymethylated bases; cuts 10 bp, 3' end from restriction site

Front 44

What is the difference between DNA and RNA bases?

Back 44

2' carbon has -H in DNA, where RNA has -OH

Front 45

Draw adenine:thymine hydrogen bond (chemical structure)

Back 45

Front 46

Draw guanine:cytosine hydrogen bond (chemical structure)

Back 46

Front 47

Describe the following mutations: 1) substitution, 2) deletion, 3) insertion, 4) frameshift

Back 47

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

Front 48

What is the ori?

Back 48

origin of DNA replication

Front 49

Function: helicase

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unwinds DNA and stabilizes replication with aid from SSB (single-strand binding) proteins

Front 50

Function: primase

Back 50

primes lagging strand synthesis by laying down short RNA complement strands

Front 51

Function: gyrase

Back 51

relieves strain induced by helicase by relaxing DNA from super-coiled conformation

Front 52

List and describe steps of transcription in eukaryotes

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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

Front 53

What is the difference between Rho-dependent and Rho-independent termination in prokaryotic transcription?

Back 53

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

Front 54

How is mRNA splicing performed?

Back 54

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

Front 55

What is the Shine-Dalgarno box? Kozak box?

Back 55

Shine-Dalgarno box refers to the 5' UTR of prokaryotic RNA transcripts

Kozak is the eukaryotic version

Front 56

Describe the mRNA:ribosome interaction during translation

Back 56

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

Front 57

What are the three stops codon?

Back 57

UGA, UAA, UAG

Front 58

What is metaphase?

Back 58

stage of cell mitosis where chromosomes are condensed and align along the metaphase plate

Front 59

What makes up the structure of a nucleosome?

Back 59

DNA and octameric complex of histones, DNA is wrapped around the complex 2-3 times

Front 60

What is the difference between exonuclease and endonuclease activity?

Back 60

Endonucleases are able to cleave the phosphodiester bond in the middle of sequences

Exonucleases must start from either 5'/3' end

Front 61

How sensitive is PAGE?

Back 61

can differentiate 1 bp difference across lanes

Front 62

What is PFGE best at resolving?

Back 62

very large DNA fragments (>50 kbp)

Front 63

What is capillary electrophoresis?

Back 63

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

Front 64

Outline the target, probe and purpose of the following:

1) Southern blot

2) Northern blot

3) Eastern blot

4) Western blot

5) Southwestern blot

Back 64

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

Front 65

Outline the steps taken to perform Southern Blot

Back 65

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

Front 66

What does branched DNA amplification target? How does it work?

Back 66

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)

Front 67

What does NASBA mean? What does it target? How does it work?

Back 67

Nucleic Acid Sequence Based Amplification;