Molecular Diagnostics exam Flashcards
In end-point PCR gel, what are the fragments that migrate past the smallest standard?
Primers and primer-dimers
During the transfer of DNA for Southern blotting, larger fragments of DNA do what?
Transfer more slowly than smaller fragments
In the denaturation step of the polymerase Chain Reaction what happens to the dsDNA?
Gets separated into ssDNA
What are the steps to southern blot procedure?
Restricted enzyme
electrophoresis
denaturation
probe hybridization
What is the signficance of the observation of circulating mRNA versus the observation of circulating DNA?
The presence of circulating mRNA indicates that a message has been transcribed and will likely result in the synthesis of new protein
Which reporter unit in real-time PCR is designed in a hair-pin structure?
Molecular Beacon
Fluorescent dye specific to dsDNA?
SYBR Green
This method exploits the natural 5’ to 3’ exonuclease activity of Taq polymerase to generate signal?
TaqMan Probe
This method utilizes specific probes, one with a 3’ fluorophore (acceptor) and the other with a 5’ catalyst for the flurorescence (donor), that bind to adjacent targets?
FRET (fluorescent resonance energy transfer
The conversion of mRNA nucleotide sequences and the transfer RNA tRNA attached amino acids into a polypeptie is referred to as what?
translation
The copying of one strand of DNA into RNA by a process similar to that of DNA replication?
Transcription
What are UV spectrophotometry, microfluidics technology, and gel electrophoresis used for?
quantitating DNA concentration
What method uses antibodies bound to the surface of a microtiter well to detect the presence of human papilloma virus?
Hybrid capture assay
Singnal amplification system based on th eproprietary cleavase enzyme?
Cleavage-based amplification
Replication of a DNA or RNA target through an intermediate RNA product?
Nucleic Acid sequence-bases amplification (NASBA)
What determines the specificity in terms of the gene that is detected in the Southern Blot method?
Labeled probe
The steps to DNA isolation?
Cell lysis
precipitation
protein digestion
nitrogens with a single ring structure?
Cystosine and Thymine (pyrimadines)
nitrogens with a double ring structure?
Adanine and guanine (purines)
This enzymes breaks the sugar-phosphate backbone of DNA?
Endonuclease
These are endonulceases that recognize specific base sequences and break or restrict the DNA?
Restriction enzymes
Denaturation temp?
annealing temp?
DNA extension temp?
Denaturation 94-96 degrees
annealing 50-70 degrees
DNA extension 72 degrees
What is DNA—>Transcription—>RNA—>translation—->protein?
Central Dogma of molecular biology
Nucleic acids migrate toward which pole in electrophoresis?
anode
What dimultaneously detects two or more different targets from one polymerase chain reaction tube?
multiplex pcr
strand of the parent double helix that is read 5’ to 3’ and replicated discontinuously?
lagging strand
strand of parent double helix that is read 3’ to 5’ and replicated continuously?
leading strand
polyadenylic acid at the 3’ terminus of mRNA
poly A tail
Intermediate products of DNA synthesis on the lagging strand
Okazaki fragments
DNA that is generated from RNA prior to amplification is called what?
Complementary DNA (cDNA)
These occur only in microorganisms, recognize sequences of 4-15 bp in length, and cleave phophodiester bonds
restriction endonucleases
The most commonly used polymerasein the PCR procedure?
Taq polymerase
Stringent hybridization conditions for southern blotting?
High temp, low salt concentration
What wavelength of light is protein absorbed in our nucleic acid suspension?
280 nm
What enzyme generates single stranded DNA from ribosomal or messenger RNA?
DNA polymerase
Which enzyme would you use to join together 2 seperate DNA fragments?
DNA Ligase
What are histone modification, DNA methylation and Gene splicing?
forms of epigenetic changes
A region of DNA present in a mature strand of mRNA and can be translated into protein?
Exon
Non coding sequences in DNA that interrupt coding sequences
Intron
Helicase, DNA template and DNA polymerasea are required for what?
DNA replication
Cytosine and Guanine have how many hydrogen bonds?
3
Adenine and thymine have how many hydrogen bonds?
2
The RNA processing sections of nucleotides are removed by:
splicing
A chromosome that has the centromere at the end of the chromosome is called:
telocentric
A chromosome that has the centromere in the middle of the chromosome
metacentric
A chromosome the entire length of which acts as a centromere
holocentric
In DNA the absorptivity constant is what?
50 ug/mL
In RNA the absorptivity constant is what?
40 ug/mL
phenomenon associated with tri-nucleotide repeat disorders of earlier onset and increasing severity of disease with successive generations?
anticipation
Method of DNA sequencing where dideocxy NTPs are incorporated into growing oligonucleotide chains, resultig in termination ddNTP’s
Dideoxy (Sanger) sequencing
consisting of many clones, often reference to lymphoid cells
polyclonal
Individual with 2 abnormal alleles, each with a different polymorphism or mutation.
Compound heterozygote
mutation that is the change of a single base?
point mutation
process of forming a double stranded molecule from a single stranded probe and a single stranded nucleic acid target based on complementary?
hybridization
gene constitutively expressed inmost cells that can serve as an internal control for reverese transcriptase PCR?
housekeeping gene
In real-time PCR, the cycle where the exponential phase of an amplification curve begins?
crossing point
proofreads newly synthesized DNA and breaks the phosphodiester bond to replace it with the correct one?
exonulease
adaptors that link condons in mRNA with amino acids?
tRNA
an isothermal amplification reaction using nick translation and strand displacement…proceeds at 1 temperature
stand displacement amplification
Target DNA is released from the cells bound to ssRNA probes. Used in the detection of HPV.
Hybrid capture signal amplification
Single strand of a DNA double helix that is not used as a template for messenger RNA synthesis
sense strand
single strand of a DNA double helix that is used as a template for messenger RNA synthesis
anti-sense strand
breakage and fusion of separate chromosomes
translocation
alteration in the nucleotide sequence that does not change the amino acid sequence
silent
alteration in the nucleotide sequence that results in the substitution of an amino acid with one of similar properties
conservative
alteration in the nuleotide sequence that results in the substitution of an amino acid with on of dissimilar properties
non-conservative or missense
alteration in the nucleotide sequence that results in the substitution of a termination codon for an amino acid codon
non sense
deletion or insertion of other than a multiple of three base pairs in coding sequence
frameshift
method used to detect sequence alterations in DNA through differences in secondary structure due to differences in the nucleotide sequence?
Single strand conformation polymorphism
polymorphism detection technique using immobilized target and sequence specific probes
allele-specific oligomer hybridization
detection of point mutations or polymorphisms in DNA with primers designed so that the 3’ most base of the primer hybridies to the test nucleotide position in the template?
sequence-specific primer
method using time of flight?
MALDI-TOF
genetic locus that differs between two individuals?
informative locus
< 1 % of the population have this
mutation
> 1% of the population have this
polymorphism
a procedure that identifies specific nucleotide sequences localized within cells in a tissue section?
FISH
in situ hybridization
What molecular mechanism accounts from the emergence of methacillian resistance to staph aureus?
mutation of the Meca gene in the DNA that alters penicillin binding protein.
Micro satellites that repeat 2-10 bps are also known as what?
STRs
mini satellites that repeat 40-500 bp in length are called what?
VNTP’s
variable number of tandem repeats
One base pair variation from a reference DNA sequence
SNP
single nucleotide polymorphism
biological properties of an organism?
phenotype
genetic DNA composition of an organism
genotype
reference size standards used in STR analysis representing all possible products (alleles) for a given locus?
allelic ladders
genetically linked set of alleles that are inherited together?
haplotype
the donor organ and the recipient are genetically different?
allograft
the level of detail with which an allele is determined?
resolution
What are the most important polymorphic loci in the MHC?
HLA-B
HLA-DRB
Chemical sequencing method based on controlled breakage of DNA?
Maxam-Gilbert method
Each nucleotide is added in turn
only 1 in 4 will generate a light signal
the remaining nucleotides are removed enzymatically
the light signal is recorded on a pyrogram
pyrosequencing
replication of a DNA or RNA target through a intermediate RNA product
transcription-mediated amplification
inheritance pattern where the child of an affected and an unaffected carrier has a 50% probability of being affected and where the child of two affected individuals has a 100% probability of being affected
Cystic fibrosis and hemochromatosis
autosomal-recessive
inheritance pattern where the child of an affected and an unaffected individual has a 50% probability of being affected
Factor V Ligand and Huntingtons Disease
autosomal dominant
Having genetic components located on the X or Y chromosome
hemophilia
sex-linked
The frequency of expression of a disease phenotype in individuals with a gene lesion
penetrance
mutated gene that promotes proliferation and survival of cancer cells
oncogene
self directed cell death
apoptosis
the normal intrachromosomal rearrangements in B and T lymphocytes as well as the abnormal interchromsomal translocation that can occur in any cell type
V(D)J recombination