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BMS 2 > Human Genome and Karyotype > Flashcards

Human Genome and Karyotype Flashcards

1
Q

Genome size
Dna, genes, #chroms
# genes in mito

A

3.2 billion bps
22,000 genes
23 pairs of chroms
37 genes known

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2
Q

Chromatid

A

After DNA is replicated, form a pair of sister chromatids attached by a centromere

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3
Q

C-value enigma

A

some single celled organism have larger genome size than humans

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4
Q

Ploidy

A

Chrome number does not correlate with genome size/complexity

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5
Q

Mechs that lead to increased genome comlpexity/size

A

Duplication of existing sequences (evidenced by multilane families)

Lateral transfer-incorporation of DNA from other species

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6
Q

RNA vs DNA

A

RNA may have preceded DNA

  • more complex and diverse in functions
  • BUT DNA is stable
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7
Q

ENCODE Project

A

Essentially mapped genome for 80 different cell types for exons, histone mods, regions where dna cleaves, binding of many tf factors

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8
Q

Encode projet conclusions

A

80% of genome is functional and noncoding regions may be more important than protein coding in determinants of health and disease

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9
Q

CTCF encriced

A

insulated-no interactions with enhancers or promoters

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10
Q

enchancers

A

open, h3k4me1, h3k28ac, bound tf’s

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11
Q

Promoters and tf start sites

A

h3k4me3, bound pol 2/3 and proximal binding tfs

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12
Q

transcribed regions

A

h3k36me3, elongationg form of polymerase, polyA+ RNA

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13
Q

Repressed

A

H3k27Me3, bound polycomb group proteins

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14
Q

Functional states of chromatin

A

cell type specific

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15
Q

Functional DNA

A

sequences that display a reproducible biochemical signiture

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16
Q

Encode on evolutionary genome

A

a lot of baggage through evolution but doesn’t hurt us enough to be eliminated through evolution

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17
Q

Variation in genome

A

Much is of unclear significance-try to find ones that affect phenotype

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18
Q

Tandem repeats

A

ancient repeats have diverged in nucleotide over time. recent rrepates have over 90% sequence identity

repeats of genes or blocks of genes

repeats homology make hot spots for recombination
-can cause inversion, duplication or deletion

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19
Q

% of genome that natural selection operates on

A

10%

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20
Q

red green color blindness

A

Recombination of duplicate genes that are almost same sequence on x chromosome

  • misalingment in meiosis followed by recombination
  • may lose a single receptor gene -cant distinguish between red and green

red(long), green(medium_)

males with deleted x have only 1 receptor-cant distinguish

21
Q

Contiguous gene syndromes

A

Microdeletion or segmental aneuplidy syndromes

recombination in large repeates deletes a block of dna with multiple genes

22
Q

Satellite sequences

microsatellites

A

short repeats

Tandem repeats of sequences a few hundred bp long-around centromeres and telomeres

Repeats of few nucleotides, copy number highly variable-used to identify parents

Called satellites because when dna fractionated-repeats form satellilite seen next to DNA peak

23
Q

Retrotransposons

A

mRNA that is reversed transcribed and put somewhere else in genome
-25% of complexity of human genome

insertion into a gene can disrupt function

24
Q

LINE, SINE, Pseudogenes

A

LINE-long interspersed nuclear elements-mRNAs encoding reverse transcriptase

SINE-copies of a short cellular RNA
-Alu sequences-most abundant-restriction site for Alu

Copies of cellular mRNAs that ar not transcribed b/c no promoter

25
Q

When should you consider diagnosis of chromosome abnormality

A

hysical or menetal dev delayed

infertitly, sponaenous abortion, stillbirth

prenancy in woen over 35

cancer

26
Q

G banding

A

cells incubated with colchicine, cells consense, stain with dye

dark-g bands

can identify chrome by size, banding pattern, centromere position

27
Q

cochiicine

A

binds tubilin, prevents spindle function, arrests cell in metaphase

28
Q

p vs q arm

A

p is short, q is long

29
Q

metacentric, sub metacentric, acro centric, telocentric

A

middle of chrome

somewhat high on chrome

very high on chrome

at end of chrome-not in humans

30
Q

g banding resolution

A

CAN ONLY SEE PROBLEMS OF MUTATIONS THAT ARE SAME AS TEST

Detects large changes in chrom structutre

lower resolution limit is like 45 genes-cant detect small changes

31
Q

FISH

A

Chromatin fixed to slide, probe binds to DNA of complimentary seqeucen

Fast when done to interphase cells-lower resolution b/c dna not condensed vs metaphase

metaphase need to amplify cell number and use colchicine

prentnatal diagnosis

NEEDS SPECIFIC PROBE
+
ONLY DETECT TO POSITION WHERE YOU KNOW PROBE BINDS
-cant rule out genetic defects elsewhere

32
Q

FISH resolution

A

better in metaphase

does not reveal single nucleotide deletion or changes somewhere else in genome

useful for detecting monosomes and translocations!
-can make more specific with more specific probe (small deletions, but not single base pair deletions)

Resolution decreases as number of probes increases

33
Q

CGH

A

Comparitive Genome Hybridization

Array of oligonucs immobilized at different positions on glass slide (mercury)-completementary to sequenced spaced across genome
-compare PCR amplified patient genome with reference

Tells deletions, duplications

Can plot to see gain/ lose of chromatin

Limitation-can detect deletions or duplications but not inversions or translocations

34
Q

CGH strength/weaknesses

A

detects very small changes in genome-anywhere

Detects only icnreases/cecreases in copy number

Cannot detect rearramgents without gain or loss (inversion/translocation)

35
Q

Human polyploidy

A

not viable

36
Q

Euplody vs aneupoidy

A

normal # vs more or less (trisomy and monosomy)

Aneuplodiy lethal for most except X, Y, small autosomes

37
Q

Trisomy 21/13 designation

A

47 XY +21 or 47 XX +13

38
Q

Kleinfelter syndrome designation

A

47, XXY

39
Q

Turner syndrome designation

A

45, X

40
Q

Translocations (2 types)

A

Recipricol

Non-recpircol

41
Q

Abnormalites in chroms

A

translatiocs, inversion, duplications, deletions

42
Q

Causes of chromosome alterations

A

dsbreaks in DNA, NHEJ, carcniogenesis, increased by radiation

43
Q

How to identify + of chromasomes

A

Number of centromeres and then identify centromere to identify chromosome

44
Q

Where are most common translocations?

A

Between afrocentric autosomal chromosomes
-conceptions with extrachroms usually die, but those with extra D or G group may survive because small

Short p arms of these chrome contain only genes for rRNA (rDNA gene copy number is very large)

45
Q

Robertsonian translocations and designation

A

45, xx, 14,21 +rob(14q, 21q)

breakpoints occur within centromeres of D and g group chromosomes, with fusion of chromosomes and loss of p arms

carrier has normal phenotype

no loss of DNA in q arms

  • short arms often lost, but nonlethal
  • also have normal chr 14 and 21 from other parent
46
Q

Results of meiosis in carrier of robertsonian translocation

A

normal

balanced carrier

trisomy 14

monosomy 14

monosomy 21

trisomy 21

at meiosis- 1 robertsonian, 1 normal chrome 14, 1 normal chrome 21

47
Q

isochromasome 21

A

both arms from 21q

viable since diploid for 21q

but gametes receive either 1 21 q or no 21 q

trisomy 21 (down syndrome or lethal) or monosomy 21 (lethal)

48
Q

Pericentric inversion

A

Dna between two breakpoints in the same arm are flipped (only in middle of chromosome but tips are okay)

BMS 2 (41 decks)

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