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Flashcards in The Human Genome and Karyotype Deck (133):
1

The amount of DNA in one copy of the genome

Genome size (C-value)

2

How many base pairs of DNA do humans have in each somatic cell of our bodies?

3.2x10^9 bp

3

How many genes do humans have?

Approximately 22,000

4

During mitosis, DNA is packaged into chromosomes. What is the chromosomal make-up of humans?

22 pairs of autosomal chromosomes and 2 pairs of sex chromosomes

5

Contain distinct DNA (containing 37 known genes) not
associated with chromosomes. It is inherited solely from the mother in humans

Mitochondria

6

Chromatin condenses into chromosomes during

Prophase of mitosis (after replication)

7

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

Centromere

8

A higher order of DNA organization where DNA is condensed at least by 10,000 times onto itself

-condensed chromatin fibers

Chromosomes

9

Long and thin uncoiled structures found in the nucleus

Chromatin

10

Compact, thick, and ribbon-like. These are coiled structures seen prominently during cell division

Chromosomes

11

Chromosomes are paired, but chromatin is

Unpaired

12

Permissive to DNA replication, RNA synthesis and recombination events

Chromatin

13

Not permissive to DNA replication, RNA synthesis and recombination events

Chromosomes

14

Generally increases with an organisms complexity

Genome size

15

Wide variations exist between genome size and organism complexity; e.g., some single-celled protists have genomes much larger than that of humans. This is called the

C-value enigma

16

Does not correlate with genome size or complexity

Chromosome number (ploidy)

17

Increased genome complexity/size arises by what two basic mechanisms?

Duplication and Incorporation (from other species)

18

In humans, which is more abundant, RNA or DNA?

RNA

19

More complex and diverse in its function and may have preceded DNA in evolution

RNA

20

Has more chemical stability and thus provides evolutionary advantages

DNA

21

Mapped the genome in 80 different human cell types for transcripts and protein-encoding exons, chromatin modification and DNA methylation, DNAse hypersensitivity, and binding of transcription factors

Encyclopedia of DNA elements (ENCODE)

22

Identifies cis-regulatory regions where the binding of regulatory factors exposed DNA to cleavage while DNA in nucleosomes is protected

DNAse hypersensitivity

23

The ENCODE project concluded that chromatin exists in

7 major functional states

24

The ENCODE project concluded that what percentage of chromatin is transcribed into RNA?

60-75%

25

The ENCODE project concluded that non-coding transcripts, many predicted to have regulatory roles, are nearly as abundant as

Protein-encoding genes

26

The ENCODE project concluded that there are only 21,000 protein coding genes, but at least 70,000 promoters and how many enhancers?

400,000 enhancers

27

Concluded that At least 80% of the genome is likely to be “functional” implying thatʻnon-coding regionsʼ may be as, or more important than, protein-encoding regions (as determinants of health and disease)

ENCODE

28

Repetitive sequences are common in the human genome and consist of

1.) Tandem repeats
2.) Short repeats
3.) Retrotransposons

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Repeats which are products of reverse transcription

Retrotransposons

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Ancient tandem repeats have diverged in nucleotide sequence over time. However, recent repeats (segmental duplications) have a sequence identity of

>90%

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Create "hot spots" for recombination, increasing the chance of structural change in chromosomes and the frequency of some genetic conditions

Repeats

32

Substrates for recombination because they are similar or identical in nucleotide sequence

Repeats

33

If sequence identity exists in more than 2 places, then what can occur between these regions?

Recombination

34

Depending on the position and orientation of the repeats, recombination between repeats may cause

Inversion, duplication, or deletion

35

Caused by recombination between duplicated genes with almost identical sequence identity on the X-chromosome

Red-green color blindness

36

In red-green colorblindness, there is a misalignment in meiosis followed by

Recombination

37

Due to the presence of three different photoreceptors in the retina, each sensitive to different wavelengths

Color Vision

38

The long (red) and medium (green) wavelength photoreceptors are encoded by genes close together on the

-The two genes differ by only a few bp

X chromosome

39

Recombination during meiosis can delete one gene from the chromosome. Males who carry a deleted X have only one receptor and thus can not distinguish

Long and medium wavelength light

40

Recombination occurs between large repeats resulting in the deletion of a block of DNA that contains multiple genes

-Ex: DiGeorge (Velocardiofacial) Syndrome and Prader-Willi and Angleman syndromes

Contiguous gene (microdeletion or segmental autoploidy) syndromes

41

Characterized by the failure of the pharyngeal pouches to develop. Results in parathyroid, thymus, and cardiac defects

DiGeorge (Velocardiofacial) Syndrome

42

Tandem repeats of sequences of a few hundred base pairs long; hundreds to thousands of copies, mostly at centromeres and telomeres.

Satellite sequences

43

Repeats of a few nucleotides, such as (CA)n dinucleotides. Common, copy number n highly variable. Widely used to identify specific chromosomes in genetic counseling, because often each of the four parental copies will be different.

Micro-Satellites

44

Satellites are called satellites because when DNA is fractionated, there is a small peak next to the DNA peak because it differs in

Base composition

45

Estimated to account for up to 25% of the increased complexity of the human genome

Retrotransposons

46

What are the main types of retrotransposons?

1.) LINE
2.) SINE
3.) Pseudogenes

47

mRNA's encoding reverse transcriptase

LINE (long interspersed nuclear elements)

48

Copies of a short cellular RNA

-Most abundant are Alu sequences

SINE (short interspersed nuclear elements)

49

The most abundant SINEs are Alu sequences, which are unique to human DNA and are named because they contain a restriction site for

Alul

50

Copies of cellular mRNAs

-not transcribed because they lack promoter sequences

Pseudogenes

51

Insertion of reverse-transcribed RNA into DNA can disrupt a gene at an

-An uncommon but well-known cause of genetic disease

Integration site

52

Analysis of the number and structure of chromosomes

Cytogenesis

53

About what percentage of people have an abnormality of chromosome number or structure?

1.5%

54

If there are problems with physical or mental development, infertility, spontaneous abortion, stillbirth, pregnancy in a woman 35 or older, or cancer, you should consider a diagnosis of

Chromosome abnormality

55

Techniques used for visual identification of chromosomes and to detect changes in their structure

Karyotyping

56

What are three karyotyping techniques?

1.) G banding
2.) Fluorescent in situ hybridization (FISH)
3.) Comparative genomic hybridization (CGH)

57

Giemsa staining creates a pattern of dark and light bands unique to each chromosome in

G banding

58

Detects changes in chromosome structure that are too small to see by G banding

-The location must be known in order to design the probe

FISH

59

Detects deletions or duplications even if their location is not known

Comparative Genomic Hybridization (CGH)

60

In G banding, cells are incubated with colchicine, which binds tubulin, prevents spindle function, and

Arrests cells in metaphase

61

Condense steadily during prolonged metaphase.

-With time, the number of cells in mitosis increases but the number of visible bands decreases

Chromosomes

62

The standard karyotype will have how many bands per haploid set of chromosomes?

500-800

63

In G banding, chromosomes are identified by

1.) Size (1 largest, 22 smallest)
2.) Centromere position
3.) Banding pattern

64

A chromosome is made up of what three regions?

1.) P (short) arm
2.) Centromere
3.) Q (long) arm

65

What are three different styles of chromosome?

1.) Metacentric
2.) Submetacentric
3.) Acrocentric

66

The centromere is located in the middle of a

ex: chromosome 3

Metacentric chromosome

67

The centromere is located above the midline, but not at the top of the chromosome in a

-Ex: chromosome 18

Sub-metacentric Chromosome

68

The centromere is located high, towards the top of the chromosome in a

-Ex: chromosome 22

Acrocentric Chromosome

69

Has the centromere at the end of the chromosome

-Not present in humans

Telocentric Chromosome

70

Chromosome bands are numbered on each arm outward from the

Centromere

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The chromosome bands are further divided with increasing

Resolution

72

Can detect structural changes regardless of the nature or location, but detects only relatively large changes in chromosome structure

G-banding

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The lower resolution limit of G banding is

One band

74

For metaphase G banding, there are about

500-800 bands

75

A single band is about

4-7 Mb (45 or so genes)

76

To detect smaller changes in a chromosome, we want to use

FISH or CGH

77

Chromatin or chromosomes are fixed to a slide and a fluorescent probe binds to DNA of the complimentary sequence

Fluorescent in situ hybridization (FISH)

78

Faster because it can be done directly on clinical samples

Interphase FISH (on Chromatin)

79

Requires culture to amplify cell number and then incubation in colchicine

Metaphase FISH (on Chromosomes)

80

Has a lower resolution because DNA is not condensed

Interphase FISH

81

Because it is faster, Interphase fish is often used for

Prenatal diagnosis

82

Interphase fish is also used to identify common

Trisomies

83

An example of a use of Metaphase FISH is screening for

DiGeorge syndrome

84

FISH only indicates that a region of DNA complementary to the probe is present. But it will not reveal a single nucleotide deletion/change in the gene or changes elsewhere in the genome. Thus FISH can not rule out a

Mutation or Small deletion in the gene

85

When using FISH, a small deletion will only be revealed with a very specific

Probe

86

Detects alterations too small to be seen by G banding but requires a specific probe and only detects the presence/absence/position of the DNA to which the probe binds

FISH

87

One problem with FISH is that single probes detect the presence of an exon or gene but cannot detect

Single nucleotide changes

88

In FISH, a family of probes can detect a single chromosome or region, but resolution decreases as the number of probes

Increases

89

An array of oligonucleotides are immobilized at different positions on a glass slide (microarray), complementary to sequences spaced across the genome in

Comparative Genome Hybridization (CGH)

90

Compares PCR-amplified patient genome (test) DNA with reference genome (control) DNA in the ability to hybridize with oligonucleotides

CGH

91

You can analyze the CGH by comparing the

Green (patients DNA) to Red (control DNA) ratios

92

For example, if the control has two DNA sequences that hybridize to oligonucleotides, but the patient (Green) experiences a deletion in one of those sequences, the green to red ratio will be

1 : 2, or 0.5 : 1

93

Detects very small changes anywhere in the genome

-i.e. you do not need to know where to look

CGH

94

A weakness of CGH is that it detects only

Deletions or duplications

95

CGH can not detect rearrangements without gain or loss, such as

Inversions or translocations

96

Refers to the chromosome number

Ploidy

97

Sperm have one copy of each chromosome, meaning they are

Haploid (N)

98

Zygotes and somatic cells contain two copies of each chromosome, meaning they are

Diploid (2N)

99

In diploid cells, the two copies of each chromosome are

Homologues (form a homologous pair)

100

Normally, one homologue is maternal, from the egg, and one is paternal, from the sperm. They carry the same genes in the same order, but not necessarily identical

Alleles

101

If the homologous chromosomes differ genetically, normally they are distributed into gametes in a 1:1 ratio. This is what gives rise to

Mendel's Laws

102

Diploid conceptions with two maternal or two paternal chromosomes are not

Viable

103

Characterized as having a normal number of chromosomes: 22 pairs of autosomes and one pair of sex chromosomes

Euploidy

104

The karyotype designation for Euploidy is

46, XX or 46, XY

105

Characterized as having missing (2N-1, monosomy) or extra (2N+1, trisomy) chromosomes

Aneuploidy

106

Aneuploidy for most chromosomes is

-exceptions: X, Y and trisomy for a few small autosomes

Lethal

107

When 2 sperm fertilize one egg resulting in 3 complete chromosome sets

-Lethal

Triploidy

108

Down syndrome in a male is indicated by

Trisomy 21

Karyotype designation: 47, XY, +21

109

Down syndrome in a female is indicated by

Trisomy 13

Karyotype designation: 47, XX, +13

110

A female with monosomy X (45, X) has

-only nonlethal monosomy

Turner's syndrome

111

When genetic material is moved from one chromosome to another

Translocation

112

What are the two types of translocation?

1.) Reciprocal
2.) Non-reciprocal

113

When 2 chromosomes exchange segments

Reciprocal translocation

114

The movement of DNA from one chromosome to another

Non-reciprocal Translocation

115

When a segment of DNA is inverted with respect to the rest of the chromosome

Inversion

116

What are three abnormalities in chromosome structure

1.) Translocation
2.) Inversion
3.) Duplication or deletion

117

When a double stranded DNA break occurs, the chromosomes are healed by recombination, NHEJ, or slower backup mechanisms. If the ends are not rejoined correctly, there will be a

Structural alteration of the chromosome

118

Structural alterations of a chromosome are important in carcinogenesis because they can alter gene structure or expression. They are increased by

Radiation

119

The general rule is that the number of chromosomes = the

Number of centromeres

120

The identity of a chromosome = the identity of its

Centromere

121

Most common translocations are between

Acrocentric autosomes

122

Breakpoints occur within the centromeres of D- and G-group chromosomes, with fusion of chromosomes and loss of p arms

-i.e. two q arms fuse together and lose their p arms

Robertsonian Translocations

123

Is Robertsonian translocation always lethal?

No, not always

124

During metaphase, the Robertsonian chromosome will pair with

2 chromosomes (1 that contains one q arms and the other containing the other q arm)

125

In Robertsonian translocation, the pairing of homologous chromosomes during metaphase will occur between

3 chromosomes (2 normal and 1 translocation)

126

A chromosome where both arms are from the q arm of chromosome 21

Isochromosome 21 (i21q)

127

Fertilization of a cell with i21q will result in either

trisomy 21 (downs) or monosomy 21 (lethal)

128

Any live-born children with i21q qill have

Down Syndrome

129

An inversion in which the break points are in different arms of the same chromosome and thus the inversion includes the centromere

Pericentric inverison

130

Inversion where the 2 breakpoints are in the same arm and thus the centromere is not included in the inversion

Paracentric inversion

131

What does 46, XY, t(1:3)(q31;q24) mean?

Male with 46 chromosomes that has a translocation between chromosomes 1 and 3, and the position of the translocation is the q31 for chromosome 1 and q24 for chromosome 3

132

What does rob(14;21) mean?

Robertsonian translocation where the q arms of chromosomes 14 and 21 are joined

133

What does 46, XY, inv(6)(p23;q21) mean

A male with 46 chromosomes has an inversion on chromosome 6 between p23 and q21, and since the inversion is in different arms, it is a pericentric inversion

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