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human genome organization Flashcards

1
Q

gene rich regions

A

chrom 19

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2
Q

gene poor regions

A

chr 13, 18, 21

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3
Q

stable regions

A

most of the genome

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4
Q

unstable regions

A

many are disease associated like
SMA: chr 5q13
DiGeorge Syndrome: chr 22q
12 diseases associated with unstable region on chr 1(1q21.1)

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5
Q

GC rich regions

A

38%

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6
Q

AT regions

A

54%

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7
Q

clustering of GC rich and AT rich regions are the basis for

A

chromosomal banding patterns

G banding

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8
Q

G staining stands for

A

giemsa staining

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9
Q

_____% of genome is translated (protein coding)

A

1.5 %

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10
Q

____% of genome is represented by genes (exons, introns, flanking sequences involved in regulating gene expression)

A

20-25

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11
Q

____ % of genes are is single copy sequences

A

50

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12
Q

______% of genes is classes of repetitive DNA

A

40-50

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13
Q

euchromatin

A

relaxed

expressing

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14
Q

heterochromatin

A

condensed

not expressing

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15
Q

genome seuqencing is focused on _______ regions

A

euchromatic

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16
Q

_______ regions are essentially unsequenced

A

heterochromatic

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17
Q

gaps can still remain in _______ regions

A

euchromatic

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18
Q

Classes of repetitive DNAs:

A
  1. Tandem repeats

2. disersed repetitive elements

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19
Q

tandem repeats:

A

satellite DNA found in different parts of genome

hotspots for

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20
Q

dispersed repetitive elements

A
  1. alu family (SINES)
  2. L1 family (LINES)
  3. Alu’s and L1’s can be of significant medical relevance
  4. retrotransposition
  5. (NAHR)
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21
Q

NAHR

A

non-allelic homologous recombination

dispersed repetitive element

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22
Q

SINE

A

short interspersed repetitive element
300bp
500,000 copies in genome
dispersed repetitive element

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23
Q

LINE

A

Long interspersed repetitive element
6 kb related members
100,000 copies in genome

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24
Q

Duplication rich genome architecture promotes _________

A

NAHR and disease

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25
segmental dynamic mutation is
nonallelic homologous recombination (NAHR) between blocks of segmental duplication during mitosis leads to micro deletion and micro duplication of the unique region bracketed by duplications. If the region contains dosage sensitive genes (ABC), disease results. if not, duplicated cur is predisposed to additional rounds of micro deletion and duplication with increased probability
26
Insertion deletions polymorphisms (indels):
1. minisatelites | 2. microsatellites (STRs)
27
minisatellites
tenderly repeated 10-100 bp blocks of DNA | VNTR (variable number of tandem repeats)
28
microsatellites (STRs)
di-, tri-, tetra-nucleotide repeats | 5 x 10^4 per genome
29
SNPS
frequency of 1 in 10^3 bp PCR detectable markers widely distributed
30
Copy number variations (CNVs)
variation in segments of genome from 200 bp-2 Mb can range from one additional copy to many array comparative genomic hybridization (array CGH)
31
Gene families are composed of
genes with big sequence similarity e.g. >85 that may carry out similar but distinct functions some are clustered and some are dispersed
32
gene families arise through
gene duplication | major mechanism to evolutionary change
33
CNV's are
primary type of structural variation CNV loci may confer 12% of genome implicated in increasingly large number of diseases
34
examples of insertions and deletions (indels)
repeats: STRs, VNTRs
35
estimated that _____% of genome is comprised of segmental duplications
5%
36
interhominoid cDNA array based comparative genomic hybridization
arrayCGH | compare human to human or normal to cancer. Can also compare human to non human
37
implications of highly dynamic genome
1. no human genome is completely sequenced and assembled 2. all regions of genome do not look/behave the same way 3. rapidly changing, complex genomic regions 4. missing heritability for many complex diseases
38
GWAS
genome wide association studies | these implicate loci that account for only a small % of expected genetic contribution
39
haploid human genome sequence is how long
3 x 10^9 bp
40
The chromosomes are found in
23 pairs: 1) 22 autosomes (1-22) 2) 1 pair of sex chromosomes (XX or XY)
41
Each chromosome is believed to consist of a _______
a single, continuous DNA double helix.
42
Genotype + environment =
Genotype + environment = phenotype
43
“α-satellite”
repeats (171 bp repeat unit) found near centromeric region of all human chromosomes; may be important to chromosome segregation in mitosis and meiosis.
44
how many new mutations per person?
30
45
what drives adaptation?
random genetic variations
46
random variation in highly ordered structure of DNA and RNA and protein almost always result in.....
deleterious consequences like genetic disease
47
clustering
non random distribution of GC and AT region is the cause for chromosomal banding
48
minisatellites
randomly repeated 10-100 bp blocks of DNA
49
minisatellite examples
VNTR (variable number of tandem repeats)
50
microsatellites
di, tri, tetra nucleotide repeats | 5 x104 per genome
51
microsatellite examples
STRPs (short tandem repeat polymorphisms)
52
single nucleotide polymorphism examples
A to G | C to A
53
SNP frequency
1 in 103 bp
54
SNP is ___ detectable
PCR
55
CNVs are
copy number variants varaition in segments of genome tom 200bp -2Mb one adds copy to many
56
CNVs found by
array compparative genomic hybridization (CGH)
57
variants can be
silent or have function effect
58
current human genome
99% of euchromatic region of genome | 241 gaps
59
tandem repeats
spread throughout genome found in 1, 9, 16 and Y a-satellite repeats near centromere
60
alu family
300 bp | 500,000 copies in genome
61
LINE family
6 kB | 100,000 copies in genome
62
dispered elements may cause disease by
insertion into genes and aberrant recombination
63
how many genes?
25,000-30,000
64
types of genes
protein coding RNA coding pseudogenes
65
advantage of gene duplication
when gene duplication, one copy is free to carry out normal function, the other copy is free to change and lead to evolution
66
missing heritability
large percentage of genetic factors of dz are yet to be found =missing heritability this is thought to be in unsequenced, dynamic portions of genome
67
how frequently SNP is likely to occur between two individuals
1 every 1000bp | 99% identical and 3 million differences
68
3 types of variation in genome
1. indertion-deletion polymorphism (indel) 2. SNP 3. CNVs
69
indels are
1. minisatellites | 2. microsatellites
70
retrotransposition many cause
insertional inactivation of genes
71
NAHR
repeats may facilitate aberrant recombination events before different copies of dispersed repeats leading to diseases

M2M exam 2 (23 decks)

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