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The Human Genome and Karyotype Flashcards

1
Q

The amount of DNA in one copy of the genome

A

Genome size (C-value)

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2
Q

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

A

3.2x10^9 bp

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3
Q

How many genes do humans have?

A

Approximately 22,000

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4
Q

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

A

22 pairs of autosomal chromosomes and 2 pairs of sex chromosomes

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5
Q

Contain distinct DNA (containing 37 known genes) not

associated with chromosomes. It is inherited solely from the mother in humans

A

Mitochondria

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6
Q

Chromatin condenses into chromosomes during

A

Prophase of mitosis (after replication)

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7
Q

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

A

Centromere

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8
Q

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

-condensed chromatin fibers

A

Chromosomes

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9
Q

Long and thin uncoiled structures found in the nucleus

A

Chromatin

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10
Q

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

A

Chromosomes

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11
Q

Chromosomes are paired, but chromatin is

A

Unpaired

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12
Q

Permissive to DNA replication, RNA synthesis and recombination events

A

Chromatin

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13
Q

Not permissive to DNA replication, RNA synthesis and recombination events

A

Chromosomes

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14
Q

Generally increases with an organisms complexity

A

Genome size

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15
Q

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

A

C-value enigma

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16
Q

Does not correlate with genome size or complexity

A

Chromosome number (ploidy)

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17
Q

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

A

Duplication and Incorporation (from other species)

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18
Q

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

A

RNA

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19
Q

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

A

RNA

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20
Q

Has more chemical stability and thus provides evolutionary advantages

A

DNA

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21
Q

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

A

Encyclopedia of DNA elements (ENCODE)

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22
Q

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

A

DNAse hypersensitivity

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23
Q

The ENCODE project concluded that chromatin exists in

A

7 major functional states

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24
Q

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

A

60-75%

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25
Q

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

A

Protein-encoding genes

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26
Q

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

A

400,000 enhancers

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27
Q

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)

A

ENCODE

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28
Q

Repetitive sequences are common in the human genome and consist of

A
  1. ) Tandem repeats
  2. ) Short repeats
  3. ) Retrotransposons
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29
Q

Repeats which are products of reverse transcription

A

Retrotransposons

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30
Q

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

A

> 90%

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31
Q

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

A

Repeats

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32
Q

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

A

Repeats

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33
Q

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

A

Recombination

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34
Q

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

A

Inversion, duplication, or deletion

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35
Q

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

A

Red-green color blindness

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36
Q

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

A

Recombination

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37
Q

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

A

Color Vision

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38
Q

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

A

X chromosome

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39
Q

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

A

Long and medium wavelength light

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40
Q

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

A

Contiguous gene (microdeletion or segmental autoploidy) syndromes

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41
Q

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

A

DiGeorge (Velocardiofacial) Syndrome

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42
Q

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

A

Satellite sequences

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43
Q

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.

A

Micro-Satellites

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44
Q

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

A

Base composition

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45
Q

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

A

Retrotransposons

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46
Q

What are the main types of retrotransposons?

A
  1. ) LINE
  2. ) SINE
  3. ) Pseudogenes
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47
Q

mRNA’s encoding reverse transcriptase

A

LINE (long interspersed nuclear elements)

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48
Q

Copies of a short cellular RNA

-Most abundant are Alu sequences

A

SINE (short interspersed nuclear elements)

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49
Q

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

A

Alul

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50
Q

Copies of cellular mRNAs

-not transcribed because they lack promoter sequences

A

Pseudogenes

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51
Q

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

-An uncommon but well-known cause of genetic disease

A

Integration site

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52
Q

Analysis of the number and structure of chromosomes

A

Cytogenesis

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53
Q

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

A

1.5%

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54
Q

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

A

Chromosome abnormality

55
Q

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

A

Karyotyping

56
Q

What are three karyotyping techniques?

A
  1. ) G banding
  2. ) Fluorescent in situ hybridization (FISH)
  3. ) Comparative genomic hybridization (CGH)
57
Q

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

58
Q

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

59
Q

Detects deletions or duplications even if their location is not known

A

Comparative Genomic Hybridization (CGH)

60
Q

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

A

Arrests cells in metaphase

61
Q

Condense steadily during prolonged metaphase.

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

A

Chromosomes

62
Q

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

63
Q

In G banding, chromosomes are identified by

A
  1. ) Size (1 largest, 22 smallest)
  2. ) Centromere position
  3. ) Banding pattern
64
Q

A chromosome is made up of what three regions?

A
  1. ) P (short) arm
  2. ) Centromere
  3. ) Q (long) arm
65
Q

What are three different styles of chromosome?

A
  1. ) Metacentric
  2. ) Submetacentric
  3. ) Acrocentric
66
Q

The centromere is located in the middle of a

ex: chromosome 3

A

Metacentric chromosome

67
Q

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

-Ex: chromosome 18

A

Sub-metacentric Chromosome

68
Q

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

-Ex: chromosome 22

A

Acrocentric Chromosome

69
Q

Has the centromere at the end of the chromosome

-Not present in humans

A

Telocentric Chromosome

70
Q

Chromosome bands are numbered on each arm outward from the

A

Centromere

71
Q

The chromosome bands are further divided with increasing

A

Resolution

72
Q

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

73
Q

The lower resolution limit of G banding is

74
Q

For metaphase G banding, there are about

A

500-800 bands

75
Q

A single band is about

A

4-7 Mb (45 or so genes)

76
Q

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

A

FISH or CGH

77
Q

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

A

Fluorescent in situ hybridization (FISH)

78
Q

Faster because it can be done directly on clinical samples

A

Interphase FISH (on Chromatin)

79
Q

Requires culture to amplify cell number and then incubation in colchicine

A

Metaphase FISH (on Chromosomes)

80
Q

Has a lower resolution because DNA is not condensed

A

Interphase FISH

81
Q

Because it is faster, Interphase fish is often used for

A

Prenatal diagnosis

82
Q

Interphase fish is also used to identify common

83
Q

An example of a use of Metaphase FISH is screening for

A

DiGeorge syndrome

84
Q

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

A

Mutation or Small deletion in the gene

85
Q

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

86
Q

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

87
Q

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

A

Single nucleotide changes

88
Q

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

89
Q

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

A

Comparative Genome Hybridization (CGH)

90
Q

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

91
Q

You can analyze the CGH by comparing the

A

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

92
Q

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

A

1 : 2, or 0.5 : 1

93
Q

Detects very small changes anywhere in the genome

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

94
Q

A weakness of CGH is that it detects only

A

Deletions or duplications

95
Q

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

A

Inversions or translocations

96
Q

Refers to the chromosome number

97
Q

Sperm have one copy of each chromosome, meaning they are

A

Haploid (N)

98
Q

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

A

Diploid (2N)

99
Q

In diploid cells, the two copies of each chromosome are

A

Homologues (form a homologous pair)

100
Q

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

101
Q

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

A

Mendel’s Laws

102
Q

Diploid conceptions with two maternal or two paternal chromosomes are not

103
Q

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

104
Q

The karyotype designation for Euploidy is

A

46, XX or 46, XY

105
Q

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

A

Aneuploidy

106
Q

Aneuploidy for most chromosomes is

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

107
Q

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

-Lethal

108
Q

Down syndrome in a male is indicated by

A

Trisomy 21

Karyotype designation: 47, XY, +21

109
Q

Down syndrome in a female is indicated by

A

Trisomy 13

Karyotype designation: 47, XX, +13

110
Q

A female with monosomy X (45, X) has

-only nonlethal monosomy

A

Turner’s syndrome

111
Q

When genetic material is moved from one chromosome to another

A

Translocation

112
Q

What are the two types of translocation?

A
  1. ) Reciprocal

2. ) Non-reciprocal

113
Q

When 2 chromosomes exchange segments

A

Reciprocal translocation

114
Q

The movement of DNA from one chromosome to another

A

Non-reciprocal Translocation

115
Q

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

116
Q

What are three abnormalities in chromosome structure

A
  1. ) Translocation
  2. ) Inversion
  3. ) Duplication or deletion
117
Q

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

A

Structural alteration of the chromosome

118
Q

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

119
Q

The general rule is that the number of chromosomes = the

A

Number of centromeres

120
Q

The identity of a chromosome = the identity of its

A

Centromere

121
Q

Most common translocations are between

A

Acrocentric autosomes

122
Q

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

A

Robertsonian Translocations

123
Q

Is Robertsonian translocation always lethal?

A

No, not always

124
Q

During metaphase, the Robertsonian chromosome will pair with

A

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

125
Q

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

A

3 chromosomes (2 normal and 1 translocation)

126
Q

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

A

Isochromosome 21 (i21q)

127
Q

Fertilization of a cell with i21q will result in either

A

trisomy 21 (downs) or monosomy 21 (lethal)

128
Q

Any live-born children with i21q qill have

A

Down Syndrome

129
Q

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

A

Pericentric inverison

130
Q

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

A

Paracentric inversion

131
Q

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

A

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
Q

What does rob(14;21) mean?

A

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

133
Q

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

A

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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