Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

CYTOGENETICS II > DNA MICROARRAY > Flashcards

DNA MICROARRAY Flashcards

1
Q

STUDY OF HEREDITY

A

GENETICS

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

It focuses primarily on the likelihood of _____________.

A

Genetics - developing cancer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

tests find ______, not diseases.

A

genetics - mutations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

STUDY OF GENES, HOW THEY INTERACT AND EXPRESSED AS A WHOLE

A

genomics

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

If genetics is the study of ______, genomics is the study of _____ and how they interact, how they are passed on from generation to generation, and how they are expressed as a whole.

A

heredity, genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Genetics and genomics are _________ that focuses on cancer itself and can help determine:

A

profiling tools

  1. prognosis (how aggressive)
  2. prediction (what is likely the benefit)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

It is an international scientific research project.

A

HUMAN GENOMICS PROJECT

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

HUMAN GENOMICS PROJECT
→ Determining the _______.
→ ldentifying and mapping all of the ______.

A

sequence of human DNA, human genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

HUMAN GENOMICS PROJECT
Key Findings:

There are ________ genes in a human
being

A

approximately 20,500

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

They are the basic physical and functional unit of heredity

A

GENES

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

They are a part of a DNA.

A

GENES

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Some genes act as instructions to make molecules called _____

A

proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Each human cell contains ___ chromosomes, and each chromosome contains _____ genes (based on the findings of the Human Genomic Project)

A

46

20,500

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

2 TYPES OF GENES

A

Structural and Regulatory Genese

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

A gene that codes for any RNA or protein product other than a regulatory factor.

A

structural genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Encode for proteins or RNA

A

structural genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Encode for mRNAs, rRNAS, and tRNAS.

A

structural genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Gene products have either structural or functional importance

A

structural genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

A gene involved in controlling the expression of one or more other genes.

A

regulatory genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Encode for transcription factors or regulatory RNA

A

regulatory genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Regulate the expression of structural genes
• Regulatory genes process the ________.
• Ensures that the appropriate genes are __________

A

regulatory genes

  • turning on and off of the gene
  • expressed at the proper time.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

EXAMPLES FOR STRUCTURAL GENES

A

Lac Z,A,Y genes of lac operon, actin gene

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

EXAMPLES OF REGULATORY GENES

A

Lac I gene, CAP gene

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

WHOLE DNA GENE 2 PARTS

A
  1. Intron

2. Exon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

portion of a gene that does not code for amino acids/ proteins

A

intron

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q
  • part of thw whole gene that are just intermissions

- They are just there for the whole DNA to have time in forming a final mature RNA.

A

intron

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

portion of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing.

A

Exons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

occurs only in a particular type of cell or

tissue where only a subset of an organism’s DNA will be expressed as mRNAs at any given time.

A

gene expression

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

The gene expression is focused on the _________ (________) where the 20,500 genes are activated simultaneously, and these genes are only activated when they are needed.

A

Central Dogma of Life, DNA -> RNA -> protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

The unique pattern of gene expression for a given cell or tissue is referred to as its __________.

*each gene has a unique pattern

A

molecular signature

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

If gene __ is activated (after the gene expression), it

means the patient has cancer. (Indication of cancer)

A

gene B

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Why is gene expression important in any

malignancy/disease?

A

The use of gene expression profiling and development of gene biomarkers/signatures for cancer allows for the diagnosis, progression and aggressiveness analyses, prognosis, and prediction of therapeutic treatment.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

MAIN TYPES OF GENE EXPRESSION ASSAYS

A
  1. Serial Analysis of Gene Expression (SAGE)
  2. Short Oligonucleotide Arrays SOA (Affymetrix)
  3. Long Oligonucleotide Arrays LOA (Agilent Inkjet)
  4. Fiber Optic Arrays FOA (Ilumina)
  5. cDNA Arrays (Brown/ Botstein)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

It does not use the whole sequence of genes; it only

uses a small part of the gene.

A

Short Oligonucleotide Arrays (Affymetrix)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Father of Microarray Technology

A

Mark Schena

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

The slide cDNA microarray which was discovered by

Brown and Botstein.

A

cDNA array

37
Q

Each slide contains multiple spots, and each spot

contains the DNA clone

A

cDNA array

38
Q

The sample used in cDNA array is usually _______

A

PCR generated

39
Q

Developed a scanner for reading the output

A

Steve Fooder

40
Q

Developed a quantitative way of monitoring Gene Expression Patterns with complementary DNA Microarray.

A

Patrick Brown and Mark Schena

41
Q

DNA Microarray is based on the ___________

A

Principle of Southern Blotting in the year 1975

42
Q

The concept of DNA Microarray began in the ______.

A

mid-1980s

43
Q

DNA microarray is also known as

A

DNA chip or Biochip

44
Q

It is a technology that can sequence thousands of genes at a time in order to quantify the expression of the said genes

A

DNA Microarray

45
Q

The bonding of probes and targets is referred to as

A

“HYBRIDIZATION”.

46
Q

This is the DNA of a sample of interest which

is compared to a reference DNA or ‘control DNA’.

A

Target DNA

47
Q

The gene that is placed into the hole in the

glass slide.

A

probe

48
Q

________ in general, are a snapshot that captures the

activity pattern of thousands of genes at once.

A

microarray

49
Q

a collection of features spatially arranged in a twodimensional grid, arranged in columns and rows.

A

the array/slide

50
Q

The slide consists of a thousand to hundreds of thousands

of spots per square inch

A

Array /slide

51
Q

Each spot holds ______ of copies of a DNA sequence from one gene

A

millions

52
Q

3 MAIN TYPES OF DNA MICROARRAY

A
  1. Spotted array
  2. In-situ array
  3. Self-assembled array
53
Q

→ These arrays use a poly-lysine coated microscope slide.

A

SPOTTED ARRAY

54
Q

A robotic arm dips a small tip into DNA and then onto the glass surface to fluorescently label the sample

A

Spotted array

55
Q

The probes need to be synthesized prior to chip preparation

A

spotted array

56
Q

First arrays to be created

A

Spotted arrays

57
Q

it is the most straightforward to use and relatively inexpensive.

A

spotted array

58
Q

Allows the user to check the purity and quantity of the DNA or cDNA to be used

A

spotted array

59
Q

can be time-consuming as the DNA or RNA have to be extracted, converted into cDNA (in the case of an RNA), and then purified.

A

Spotted array

60
Q

These arrays use light and photolithography to create

probes on chips.

A

In-Situ Array

61
Q

These probes are oligonucleotides that match down sequences of targeted DNA

A

IN-SITU ARRAY

62
Q

These arrays are faster than spotted arrays and do not need cDNA handling; it only requires the target sequence to be known.

A

In-Situ Array

63
Q
  • have higher sensitivity

- are costly and require specialized machinery to synthesize many arrays themselves

A

In-Situ Array

64
Q

These arrays are fiber optics.

A

Self-assembled array

65
Q

DNA is assembled on small polystyrene beads.

A

SELF-ASSEMBLED ARRAY

66
Q

Some versions contain wells already pre-made in a glass to hold the beads.

A

SELF-ASSEMBLED ARRAY

67
Q

The beads are encoded with different combinations of fluorophore so that the randomly assembled oligos are identified by their specific combinations.

A

SELF-ASSEMBLED ARRAY

68
Q

2 COMMON METHODS OF DNA MICROARRAY

A
  1. Glass Slide cDNA microarray

2. DNA chip (oligonucleotide) Microarray

69
Q

→ Conventional method.

A

Glass Slide cDNA Microarray

70
Q

First type of DNA Microarray technology developed.

A

Glass slide cDNA Microarray

71
Q

Invented by __________ & his colleagues at Stanford University.

A

Glass slide cDNA microarray- Patrick Brown

72
Q

Uses a robotic device which deposits (spots) a nanoliter sample of DNA onto a coated microscopic glass slide (Spot size: 50-150 micrometer in diameter).

A

Glass slide cDNA microarray

73
Q

The slide is usually made commercially and is made of glass/silicon/nylon.

A

Glass slide cDNA microarray

74
Q

Each slide contains thousands of spots, and each spot contains a probe for a different gene

A

Glass slide cDNA microarray

75
Q

→ Probes can attach to the slide by robotic means.

A

Glass slide cDNA microarray

76
Q

ADVANTAGES:
• Relatively affordable with a ____ cost.
• It requires _______.
• Prior knowledge of sequence is _______.
• Good choice for ______ discovery.
• Necessary clone sets are available for numerous
organisms (_______)

A

Glass slide cDNA microarray

  • lower
  • no specialized equipment
  • not necessary
  • new gene
  • humans, mice, rats
77
Q

DISADVANTAGES
• Requires ______ for synthesizing & purifying DNA solutions before microarray fabrication.
• _______ of probe (Slide DNA) as compared to oligonucleotides array.
• _________ may occur due to common sequences from the same gene family

A

Glass slide cDNA microarray

  • intensive labor
  • Low density
  • cross hybridization
78
Q

______ are high-precision robots with metal pins that dip into DNA solution and taps down on the glass
slide.

A

Microarray spotters

79
Q

Glass slides cDNA microarrays uses ______
• DNA spotting done by _____ arm using multiple pins.
• DNA in a ____ plate.
• DNA is usually _______.
• ______ can also be spotted.

A

spotting arrays

  • robotic
  • microtiter
  • PCR amplified
  • oligonucleotides
80
Q

The process is done by prefabricating or synthesizing single-stranded oligo.

A

DNA Chip (Oligonucleotide) Microarray

81
Q

Since oligos are usually ____, the density of these arrays is much higher.

A

short - DNA Chip (oligonucleotide) microarray

82
Q

DNA Chip (Oligonucleotide) Microarray is traditionally called

A

‘Gene Chips’ (Gene Chip Array) by

commercial suppliers, such as Affymetrix, Agilent

83
Q

ADVANTAGES:
• Fast
• Specific
• Reproducible

A

DNA chip microarray

84
Q

DISADVANTAGES
• In-situ oligonucleotide array formats tend to have _______ specialized equipment to carry out hybridization, staining of label, washing, and quantitation
process.

• Short sequences (oligonucleotides 10-15 base pair only) used on the array have __________ compared with glass cDNA microarrays.

A 
DNA chip (oligonucleotide) Microarray
expensive, decreased sensitivity/binding
85
Q

DNA MICROARRAY (Procedure)

A
  1. Collection of samples
  2. Isolation of mRNA
  3. Creation of Labeled DNA
  4. Hybridization
  5. Microarray scanner
  6. Analyzation of Data
86
Q

COLLECTION OF SAMPLES

Samples which can be collected:

A

a. peripheral blood
b. aspirate fluid
c. swab sample
d. lavages
- any cells that have DNA can act as sample

87
Q

ISOLATION OF mRNA

  • Extract the RNA from the samples. Using either a column or a solvent such as ________
  • After isolating the RNA, we need to isolate the ____ from the rRNA and tRNA. The mRNA has a poly-A tail, so we can use a column containing beads with poly-T tails to bind with the mRNA.
  • Rinse with _____ to release the mRNA from the beads. In turn, the buffer disrupts the Ph, disrupting hybrid bonds
A

phenol chloroform, mRNA, buffer

88
Q

CREATION OF LABELLED DNA

• Add a labeling mix to the RNA. The labelling mix contains poly-T primers, reverse transcriptase (to make cDNA), and fluorescently dyed nucleotides

  • Add Cyanine-3 (______) to the healthy cells.
  • Add Cyanine-5 (______) to the cancerous cells.
A

fluoresces green, fluoresces red

CYTOGENETICS II (2 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions