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Genetics Test 5 > 39 Biotechnology > Flashcards

39 Biotechnology Flashcards

1
Q

FISH

A

a desired sequence is labeled with a fluorescent tag; the DNA is denatured and then allowed to hybridized with the chromosome; the flurescent tag appears wherever the sequence is found

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2
Q

what allows the visualization of the location of a desired DNA sequence on a spread of chromosome?

A

FISH

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3
Q

What allows us to see where a gene is expressed?

A

reporter gene

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4
Q

two examples of reporter genes

A

luciferase from fireflies and GFP from jellyfish

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5
Q

Benefit of reporter genes

A

since we can see where the gne is expressed it allows us to conduct studies on different regulatory sequences such as promoters and enhancers to see the effect of altering these sequences on gene expression based on monitoring the expression of the luciferase production

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6
Q

GFP

A

green flourescent protein - from jellyfish, will fluoresce under UV light - often joined with protein of interest allowing us to see where the protein is expressed throughout the organism

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7
Q

microarray analysis

A

allows comparision of the expression of a set of genes (compare mRNA) from different cell types

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8
Q

describe an example of microarray analysis

A

mRNA was isolated from cancerous andnoncancerous cells from women with breast cancer, the mRNA was converted to cDNA and labeled as red or green; it was incubated with the microarray chip whicha llowed it to bind to complementary sequences on the green chip; the computen analyzes which genes produce the mRNA in the cancerous cells compared to those produced by the noncancerous cells. Found overexpression or underexpression of some genes in the cancerous cells compared to noncancerous cells.

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9
Q

examples of gene products manufactured by bacteria and used as therapeutic proteins

A

human growth hormone, insulin, blood clotting factors

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10
Q

production of therapeutic proteins

A

coding sequences are put under a bacterial promotor and introduced into the bacteria via plasmid vectors

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11
Q

examples of gene products manufactured by bacteria and used for industrial applications

A

rennin for cheese, enzymes like bacterial proteases for detergents, meat tenderizers, amylases to degrade complex sugars

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12
Q

genetically modified crops are an example of?

A

transgenic plants

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13
Q

forward genetics

A

start with a mutant phenotype and seek out the gene that causes that phenotype; uses chromosome mapping to identify the gene

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14
Q

reverse genetics

A

start with a DNA sequence/genotype, alter its function or prevent its expression and observe the effects of the phenotype; frequently use transgenic organisms

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15
Q

knock-out mice

A

mice in which a gene has been turned off allowing the function of the gene to be assayed as we can look at the different in phenotype in the WT and knockout mice

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16
Q

knock down

A

altering the level of expression witout completely knocking out the gene; useful when completely knocking out the gene is not compatible with life - RNAi is used to decress the expression by decreasing the translation of or causing the degradation of mRNA

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17
Q

example of usage of knockdown mechanism

A

siRNA for ApoB gene in monkeys knocked down expression of ApoB reducing total level of cholesterol

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18
Q

crRNA

A

naturally occuring in bacteria to prevent invasion of bacteriophages - can be modified to alter gene sequences which has the potential to repair mutant sequences, add missing genes, or inactivate bad genes

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19
Q

gene therapy

A

introducing functional copies of a gene into individuals who have only defective copies of that gene

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20
Q

transgene

A

the introduced copy of the gene in gene therapy - in successful therapy will make the missing gene product and restore normal phenotype which may only occur in somatic cells

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21
Q

somatic gene therapy

A

treats, but does not cure the disease - all current gene therapies are of this type - nonheritable

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22
Q

germ-line gene therapy

A

would result in a heritable change and comes with moral and ethical considerations - do not currently have the ability to do this

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23
Q

What type of virus is used to introduce genes into a cell for gene therapy?

A

retroviral vectors

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24
Q

describe introduction of gene into cell for gene therapy

A

retroviral vector puts the transgene into the DNA of the host cell. After the transgene gets into a cell, it is transmitted to all progeny cells in the cell lineage by mitosis

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25
potential problem with transgene
it may integrate in a way that disrupts the function of another gene
26
Other, non-retroviral, mechanisms for introducing a gene into a cell
direct injection, liquid capsules, nanoparticles, etc - can also deliver genome editing machinery like CRISPR
27
immune deficiency gene therapy trial
blood cells can be removed and targeted by retroviruses to deliver WT copy of the gene - being done in Severe Combined Immune Deficiency and Adenosine deaminase deficiency
28
hereditary blindness gene therapy trial
eye is accessible and partially protected from the immune system - a study with 9 patient showed improvement
29
cancer gene therapy trial
clinical trial in leukemia where patients immune cells were removed and modified to attack cancerous cells putting ~half into remission
30
Examples of gene therapy trials
immune deficiences, hereditary blindness, cancer, hemophilia B
31
hemophilia B gene therapy trial
men treated with gene therapy to eliminate need for standard, weekly treatment - 1 dose of gene therapy for engineered clotting factor
32
NIH requirements for gene therapy
gene must be cloned, well characterized, and available in pure form; an effective method must be available for delivering gene to desired cells and/or tissues; the risks must be careful evaluated and be shown to be minimal; disease cannot be treatable by other methods; data from preliminary animal/human cell trial must indicate the therapy should be effective
33
genetics
the study of heredity and the ariation of inherited characteristics
34
genomics
field of genetics that attempts to understand the content, organization, function, and evolution of genetic information contained within and between whole genomes
35
three maps correlated in genomics
genetic, cytological, and physcial chromosome maps
36
genomics involves
collecting sequence data, correlating genetic, cytological, and physical chromosome maps, and identifying DNA sequences that contains genes of interest in the genome and then analyzing the function of those gene products
37
genetic map
constructed from recombination frequencies in units of centimorgans
38
cytological maps
involves that banding patterns on the chomsome and are based on chromsome staining
39
physical maps
molecular distances in base pair, kilobases, megabases - often show restriction enzyme recogniztion sites, locations of particular clones or sequences-tagged sites
40
1000 bp =
1 kilobase - kb
41
1 million bp =
1 megabase pair - mb
42
1 CM is about
1 mb
43
why do different physical maps result in different distances between sites?
partly due to non-uniform amount of recombination along ht elength of the chromosome and due to a non-uniform amount of coiling and uncoiling along the length of the chromosome
44
anchor marker
help to relate maps to one another - mapped both genetically and physically so can be used to correlate genetic and physical maps
45
two examples of anchor markers
STS and EST
46
STS
sequence-tagged sites - short unique DNA sequences used to link physical and genetic maps - they are hybridized to overlapping clones on physical maps and are hybridized to cytological maps using in situ hybridization to anchor map types
47
EST
expressed-sequence tags - short cDNA sequences that are used to link genetic and physical maps. These cDNA sequences are used as hybridization probes to anchor maps
48
Which type of anchor marker contain actively transcribed areas of the chromosome?
EST - STS may not be transcribed
49
Contig
overlapping sets of clones arranged in a way that gives a physical map of part of a chromosome
50
the two approaches to genome sequencing
map-based sequencing and whole genome shotgun approach
51
map-based sequencing
classic approach - make genomic library; fingerprint library and orient clones relative to each other; screen the livrary with markers that wllow you to relate it to the recombinant map; map-based sequencing relies on detailed genetic and physical maps to align sequence fragments
52
whole genome shotgun approach
modern approach - small-insert clones/plasmids prepared directly from genomic data and sequences; computer programs assemble by examining overlap; highly automated
53
method used by NIH for genome project
map-based
54
method used by Celera for genome project
whole genome shutgun
55
Think of map based approach as?
aligning fragments along the chomosome and mapping each and combining the maps to give the map of the chromosome
56
Think of shotgun approach as?
blasing the DNA into pieces, sequencing the pieces, and then combining the sequences using powerful computer analysis
57
What combines computer science and biology
bioinformatics
58
Goals of bioinformatics
maintaining and analyzing data bases of sequence data; developing software to mine information from big data sets; comparing structural and functional features of DNA sequences and resulting proteins; determining evolutionary relationships among genomes
59
orthologs
homologous sequences found in different specieis
60
paralogs
homolgous gene in the same species that arrive through gene duplication
61
GWAS
genome-wide association studies - look for non-random association between the presence of a trait and alleles at many different loci scattered acros the genome
62
GWAS are especially useful for identifying?
QTLs
63
QTL
quantitative trait loci
64

simple process of GWAS

find associations between molecular markers and a phenotype, then look for candidate genes near the marker that may affect the trait, then validate the biological information showing there is a true causative relationship and not just correlation

65
a specific site in the genome where the DNA base varies in at least 1% of the population
SNP
66
how many SNPs are in the human genome
~10 million
67
haplotype
a sequence of SNP patterns along the length of a chromosome
68
tagSNPs
the few SNPs used to identify a haplotype
69
goal of SNPs in association studies
correlate presence or absence of specific SNP or SNP haplotype with the presence or absence of a genetic disorder
70
advantage of using SNPs in association studies
they identify DNA sequence differences between individuals more quickly and easily than sequencing the entire genome
71
problem with using SNPs in association studies
correlation is not causation - they only providing starting point
72
personalized medicine and warfarin
patients are genotyped for two genes to help determine the most effective dose
73
GINA
genetic information nondiscrimination act health insurance companies cannot decrease coverage or increase rates based on results of genetic tests employers cannot discriminate based on result neither can require genetic testing

Genetics Test 5 (5 decks)

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