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RESET - MOLBIO PRELIMS > 4.5 LEC > Flashcards

4.5 LEC Flashcards

1
Q

Which hybridization method is used when determining target size is not required?

A

Dot/Slot blots

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2
Q

What types of samples are most efficiently analyzed using dot or slot blots?

A

Less complex samples (cloned plasmids, PCR products, selected mRNA)

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3
Q

What control is necessary to ensure proper interpretation in dot or slot blot expression analysis?

A

Amplification or normalization control

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4
Q

What serves as the baseline for interpretation in dot or slot blot hybridization assays?

A

Negative control (DNA without the targeted sequence)

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5
Q

What is a key advantage of slot blots over dot blots for quantification?

A

More accurate quantification by densitometry scanning

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6
Q

What can be used for depositing the target DNA or RNA onto the membrane in dot/slot blots?

A

Various devices, including vacuum systems or a pipet

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7
Q

Why are dot blots especially useful for mutational screening?

A

Useful for multiple qualitative analyses where many targets are compared

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8
Q

What type of technology allows for the simultaneous study of large numbers of targets or samples?

A

Array technology

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9
Q

What type of arrays are used to study gene amplification or deletion?

A

Comparative genome hybridization arrays

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10
Q

Which arrays are applied to the analysis of gene expression, such as RNA or protein?

A

Expression arrays

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11
Q

Name four approaches to array technology

A

Macroarrays, microarrays, high-density oligonucleotide arrays, microelectronic arrays

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12
Q

What is the primary advantage of macroarrays over Northern and Southern blots?

A

Larger sample capacity.

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13
Q

What is a limitation of dot and slot blots regarding the number of genes?

A

Single gene testing.

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14
Q

Array technique where unlabeled probes are immobilized on the membrane, and the test sample is labeled for hybridization.

A

Reverse dot blot technique.

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15
Q

Type of blot that allows testing and analyzing larger numbers of samples simultaneously.

A

Macroarrays

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16
Q

Type of signal typically used to detect hybridization in macroarrays.

A

Radioactive or chemiluminescent signals.

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17
Q

Device used to read the hybridization of labeled sample material in macroarrays.

A

Phosphorimager

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18
Q

Material that replaced nitrocellulose or nylon membranes for producing arrays in 1987.

A

Treated glass.

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19
Q

Technology that allowed the evolution of macroarrays into microarrays by depositing very small target spots.

A

Improved spotting technology.

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20
Q

Maximum number of targets that can be screened simultaneously on a microarray.

A

Tens of thousands.

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21
Q

Size of the glass substrate used for microarrays compared to a common laboratory item.

A

Microscope slide.

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22
Q

System used to automate the deposition of spots on microarrays.

A

Arrayers

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23
Q

Number of spots that automated systems can place on a glass substrate.

A

More than 80,000 spots.

24
Q

Year the first automated arrayer was described by Patrick Brown.

A

1995

25
Q

Institution where the first automated arrayer was developed.

A

Stanford University

26
Q

Technology used by the first automated arrayers to place probe material.

A

Pen-type contact

27
Q

Type of printing systems incorporated into modified arrayers for target deposition.

A

Ink-jet printing systems

28
Q

Methods of expulsion used in ink-jet printing systems for target material.

A

Thermal, solenoid, or piezoelectric

29
Q

What replaces the larger nitrocellulose membrane in microarrays?

A

Glass microscope slide.

30
Q

What is the common term used for the glass slide carrying the array of targets?

A

Chip

31
Q

What types of targets are usually immobilized on the glass slide of a microarray?

A

DNA (cDNAs, PCR products, or oligomers).

32
Q

How are targets typically arranged on a microarray chip?

A

In triplicate and spaced across the chip.

33
Q

What are test samples usually generated from in microarray experiments?

A

cDNA generated from sample RNA

34
Q

Besides cDNA, what other types of test samples can be used in microarrays?

A

Genomic DNA, RNA, or protein.

35
Q

What is the field that studies the entire genome or sets of related genes?

A

Genomics

36
Q

What term describes the complete set of transcripts encoded by a genome?

A

Transcriptome

37
Q

What term refers to the set of encoded proteins in an organism?

A

Proteome

38
Q

Who predicted that the proteome is likely to be 10 times more complex than the genome?

A

Stanley Fields

39
Q

What is the study of entire sets of proteins called?

A

Proteomics

40
Q

What technologies facilitate the study of proteomics?

A

Array technology and mass spectrometry

41
Q

What method is used to deposit targets for array analysis directly on glass or silicon support?

A

DNA synthesis

42
Q

What technology allows for the synthesis of short oligomers (10 to 25 bases long) on high-density arrays?

A

Proprietary photolithography techniques.

43
Q

What type of arrays are used for mutation and polymorphism analysis, DNA methylation analysis, and sequencing?

A

High-density oligonucleotide arrays.

44
Q

What is required for sample preparation in array analysis for reading microarrays?

A

Fluorescent labeling of the test sample.

45
Q

What method is frequently used for labeling RNA in array analysis?

A

Synthesis of cDNA or RNA copies with labeled nucleotides

46
Q

What are arrays used to assess gene expression classified as?

A

Expression arrays

47
Q

What technique is designed to test DNA for deletions and amplifications in comparative genome hybridization?

A

Array CGH (comparative genome hybridization).

48
Q

What advantage does array CGH provide over traditional cytogenetic analysis?

A

Higher resolution and more defined genetic information.

49
Q

What is necessary for reading microarrays?

A

A fluorescent reader and analysis software.

50
Q

In bead array technology, where are the probes immobilized?

A

beads

51
Q

What allows hybridization of targets in bead array technology?

A

complementary base pairing

52
Q

How can multiple suspensions be tested simultaneously in bead array technology?

A

Using a 96-well plate.

53
Q

How are different probes on beads distinguished in bead array technology?

A

color-coding the beads with a particular shade of red fluorescent dye.

54
Q

What color dye is used to label the sample in bead array technology?

A

Green dye

55
Q

For what types of targets is bead array technology used?

A

Protein and nucleic acid targets

56
Q

What clinical applications are available for bead array systems?

A

Tests for infectious diseases and tissue typing.

RESET - MOLBIO PRELIMS (16 decks)

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