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Genetics > The OMICS > Flashcards

The OMICS Flashcards

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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
Q

what type of stain is used in PCR to visualize agarose gel electrophoresis under UV light

A

ethidium bromide

26
Q

how many locus can be tested at a time southern blot and PCR

A

southern blot - one

PCR - many

27
Q

in PCR how must the primer be placed

A

flanking the repeat area

28
Q

example of multiplex PCR

A

STR/VNTR PCR genotyping

29
Q

ways in which gene duplication (chromosomal duplication/ gene amplification) can occur

A

error in homologous recombination, retrotransposition event, duplication of an entire chromosome

30
Q

engine of evolution

A

gene duplication

31
Q

provides a mechanism for genetic disorder because of inappropriate crossing during meiosis

A

gene duplication

32
Q

why are blue color abnormalities rare?

A

not located on the X chromosome with red and green

33
Q

unequal intragenic recombination between a pair of X chromosome during meiosis

A

red green color blindness

34
Q

normal individuals have how many red and green color genes

A

1 red and 1, 2, or 3 green color pigments genes on the X chromosome

35
Q

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?

A

processed pseudogene

36
Q

three main types of microarray

A

CGH, SNP, and cDNA

37
Q

which ones are chromosomal microarray analysis

A

CGH and SNP

38
Q

which microarray is used for comparing one genome to another

A

CGH

39
Q

used in pediatrics and diagnosing developmental abnormalities

A

CGH

40
Q

medical use of SNP

A

single nucleotide polymorphism so may inform haplotypes or pharmacogenomics

41
Q

combination of alleles at different chromosomal loci that are transmitted together

A

haplotype

42
Q

enable faster identification of disease genes by tracking markers

A

haplotype

43
Q

how many locus or loci can haplotypes be

A

one locus, several loci, or even an entire chromosome

44
Q

data collection tool for haplotype

A

SNP Chip

45
Q

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.

A

HapMap

46
Q

what does Genetic Wide Association Studies (GWAS) uncover

A

genetic determinants of multifactorial diseases

47
Q

Created by scanning 1000’s of SNP among 1000’s of people

A

GWAS

48
Q

Use of cDNA microarrays to determine the genes expressed

A

transriptome

49
Q

all mRNA in a particular cell under a particular condition

A

transcriptome

50
Q

how does transcriptome work

A

Isolate mRNA

51
Q

what do the colors mean in transcriptome? (colors might change from experiment to experiment)

A

red - up regulation
green - down regulation
black - similar expression

52
Q

what is an attempt to look at the protein fingerprint of a biological sample

A

proteomics

53
Q

challenge in proteomics

A

identifying proteins that are present at low concentration because high abundance proteins hamper detection of proteins that are scarce

54
Q

how does isoelectric focusing work

A

proteins migrate during isoelectric focusing until the protein has no net charge

55
Q

what happens after isoelectric focusing

A

standard polyacrylamide gel is used to separate based on size

56
Q

who is attempting to map all of the cytidines that are methylated in the human genome and where aberrant methylation may be pathogenic

A

human epigenome project

57
Q

Methylation of CpG islands are associated with

A

reduced gene expression of nearby genes

58
Q

Fragile X is a result of

A

excessive methylation patterns (CG gets methylated)

59
Q

Fragile X leads to what?

A

reduced gene expression of FMR1 gene since it is excessive methylation

60
Q

what causes fragile X?

A

combination of genome duplication and epigenetic control

Genetics (19 decks)

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