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The OMICS Flashcards

1
Q

Whose goals are to…
• Determine entire sequence of human genome
• Identify and map the genes in the human genome
• Find single nucleotide polymorphisms
• Address and predict ethical issues associated
• To deal with unanticipated ethical issues

A

human genome sequence effort

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2
Q

steps to sequencing

A

DNA extraction –> DNA fragmentation –> Clone into vectors –> transform bacteria, grow, isolate vector DNA, sequence the library –> assemble contiguous fragments

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3
Q

was genome mapped prior to sequencing

A

yeah

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4
Q

what does annotation mean

A

identifying the function

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5
Q

regulatory domains

A

TATA boxes, C-G rich region

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6
Q

start and stop sites are in same frame as what?

A

associated splicing and tailing sequences

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7
Q

do open reading frames always have a sequence that will make a protein

A

no

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8
Q

what can the annotation process miss?

A

• Very small ORFs (open reading frames)
• Small genes within larger genes
• Genes on opposing DNA strands
• Gene that are not translated into protein
– (some RNA molecules)
• Other unknown RNA species
• It is difficult to predict splice variants

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9
Q

does the size of chromosome always correlate with the number of genes

A

nah

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10
Q

what chromosome correlate with trisomy and also have the least amount of genes

A

13, 18, 21

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11
Q

amount of genes we have

A

20,000 - 25,000

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12
Q

why doesn’t gene number correlate with the number of proteins produced?

A

alternative splicing, RNA editing, post translational modifications

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13
Q

percent of our genome that is repetitive sequence

A

50%

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14
Q

difference between STR and VNTR

A

STR - di, tri, or tetra nucleotide repeats

VNTR - slightly longer repeats

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15
Q

what are transposons

A

LINES and SINES

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16
Q

transposons are associated with what type of sequence

A

Alu sequence

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17
Q

what are the types of pseudogenes

A

vestigal genes (now dominant), duplicated genes that are not expressed, processed pseudogenes

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18
Q

genes without introns that are typically not expressed

A

processed pseudogene

basically mRNA turned into DNA then integrated into new chromosomal site

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19
Q

what does processed pseudogene have at its 3’ end

A

A rich tract

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20
Q

type of pseudogene - humans have the gene for vitamin C but it does not function

A

vestigial gene

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21
Q

type of pseudogene - one of the globin genes in the beta globin locus is not expressed

A

duplicated gene

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22
Q

most repetitive DNA in the genome

A

transposons

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23
Q

two ways that transposons can lead to disease

A

1) jumping gene can integrate into critical spot in genome, disrupt the gene, then cause disease
2) misalignment during meiosis and gene disruption

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24
Q

what do crime investigators and paternity suits use to determine identity

A

STR (most importantly) and VNTR

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25
what type of stain is used in PCR to visualize agarose gel electrophoresis under UV light
ethidium bromide
26
how many locus can be tested at a time southern blot and PCR
southern blot - one | PCR - many
27
in PCR how must the primer be placed
flanking the repeat area
28
example of multiplex PCR
STR/VNTR PCR genotyping
29
ways in which gene duplication (chromosomal duplication/ gene amplification) can occur
error in homologous recombination, retrotransposition event, duplication of an entire chromosome
30
engine of evolution
gene duplication
31
provides a mechanism for genetic disorder because of inappropriate crossing during meiosis
gene duplication
32
why are blue color abnormalities rare?
not located on the X chromosome with red and green
33
unequal intragenic recombination between a pair of X chromosome during meiosis
red green color blindness
34
normal individuals have how many red and green color genes
1 red and 1, 2, or 3 green color pigments genes on the X chromosome
35
Sequence analysis of a genome revealed a locus that had sequence homology with a gene involved in fatty acid metabolism. This sequence did not have a promoter, and it did not contain any introns. How do we best describe this locus?
processed pseudogene
36
three main types of microarray
CGH, SNP, and cDNA
37
which ones are chromosomal microarray analysis
CGH and SNP
38
which microarray is used for comparing one genome to another
CGH
39
used in pediatrics and diagnosing developmental abnormalities
CGH
40
medical use of SNP
single nucleotide polymorphism so may inform haplotypes or pharmacogenomics
41
combination of alleles at different chromosomal loci that are transmitted together
haplotype
42
enable faster identification of disease genes by tracking markers
haplotype
43
how many locus or loci can haplotypes be
one locus, several loci, or even an entire chromosome
44
data collection tool for haplotype
SNP Chip
45
catalog of common genetic variants that occur in human beings. It describes what these variants are, where they occur in our DNA, and how they are distributed among people within populations and among populations in different parts of the world.
HapMap
46
what does Genetic Wide Association Studies (GWAS) uncover
genetic determinants of multifactorial diseases
47
Created by scanning 1000’s of SNP among 1000’s of people
GWAS
48
Use of cDNA microarrays to determine the genes expressed
transriptome
49
all mRNA in a particular cell under a particular condition
transcriptome
50
how does transcriptome work
Isolate mRNA
51
what do the colors mean in transcriptome? (colors might change from experiment to experiment)
red - up regulation green - down regulation black - similar expression
52
what is an attempt to look at the protein fingerprint of a biological sample
proteomics
53
challenge in proteomics
identifying proteins that are present at low concentration because high abundance proteins hamper detection of proteins that are scarce
54
how does isoelectric focusing work
proteins migrate during isoelectric focusing until the protein has no net charge
55
what happens after isoelectric focusing
standard polyacrylamide gel is used to separate based on size
56
who is attempting to map all of the cytidines that are methylated in the human genome and where aberrant methylation may be pathogenic
human epigenome project
57
Methylation of CpG islands are associated with
reduced gene expression of nearby genes
58
Fragile X is a result of
excessive methylation patterns (CG gets methylated)
59
Fragile X leads to what?
reduced gene expression of FMR1 gene since it is excessive methylation
60
what causes fragile X?
combination of genome duplication and epigenetic control

Genetics (19 decks)

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