CMMB 413 midterm 1 Flashcards
1
Q
q banding
A
- used to detect heteromorphism (when homologous pairs are not identical)
2
Q
R banding
A
- reverse of G-banding
- specimens heated before staining (reverses banding pattern so AT is light and GC is dark)
- used to analyze distal ends of chromosomes
3
Q
G banding
A
-dark regions = AT
- light regions = GC
- most commonly used method
4
Q
C banding
A
- involving Xylene substitute
- used for staining centromeric regions or regions containing constitutive heterochromatin
- increased resolution
- can be used to detect pericentric (cuz its an inversion around the centromere)
5
Q
constitutive heterochromatin
A
hyper condensed chromatin that lies near the centromere, late replicating, C-banding positive, highly repetitive DNA
6
Q
prometaphase banding
A
- uses G or R banding to stain at prometaphase stage
- useful for identifying subtle structural abnormalities and a higher number of bands are visible (increased resolution)
7
Q
trisomy
A
extra copy of a chromosome
8
Q
triploidy
A
3 sets of chromosomes
9
Q
anueploidy
A
extra or missing number of chromosomes
10
Q
tetraploidy (4n)
A
two extra sets of chromosomes
11
Q
what is SKY useful for?
A
to identify abnormal chromosomes with pieces of different chromosomes, uses 24 different coloured probes to observe each diff chromosome
12
Q
what are the steps in molecular cloning?
A
- isolate desired DNA fragment
- Use restriction endonuclease (EcoRI) to create sticky ends that will allow all the different types of pieces of the final recombinant DNA molecule to fit together easily.
- use DNA ligase to attach desired DNA fragment and antibiotic resistance to sticky ends of the vector
- Use electrophoresis or heat shocking to insert vector into bacterial cells
- culture cells in media, select for cells containing antibiotic resistance carrying the vector
13
Q
cDNA
A
A collection of coding DNA synthesized from mRNA template using reverse transcriptase
14
Q
cDNA library
A
combination of cDNA fragments inserted into a collection of vectors
15
Q
nucleic acid hybridization
A
- establishing a sequence specific interaction btw 2 or more complementary strands of nucleic acids into a single complex
- same method as FISH but with whole strands
16
Q
what’s the biggest advantage to CGH?
A
dont need to culture anything
17
Q
what are two neurodevelopmental disorders caused by MECP2 gene mutations?
A
- gof = MECP2 duplication syndrome
- lof = rett syndrome
18
Q
whats accounts for most structural abnormalities in chromosomes?
A
rearrangement caused by chromosome breakage - generally occurring during cross over
19
Q
whats accounts for most structural abnormalities in chromosomes?
A
rearrangement caused by chromosome breakage - generally occurring during cross over
20
Q
mosaicism
A
a mutation occurs in one cell of the developing embryo
21
Q
dicentric chromosome
A
chromosome with 2 centromeres
22
Q
Pseudodicentric chromosome
A
exist as functionally monocentric (pseudodicentric) chromosomes with inactivation of one of the centromeres
23
Q
what is responsible for formation of marker/ring, iso, dicentric chromosomes
A
unbalanced rearrangments
24
Q
what type of banding approach can be used to detect pericentric inversion? paracentric?
A
peri: c banding
para: any banding or FISH
25
the exchange of chromosome segments btw 2 non-homologous chroms
chromosomal translocations (reciprocal or Robertsonian)
26
what is the lifetime frequency for having a genetic disease?
67%
27
what fraction of the population will have a genetic disorder? (not counting multifactorial diseases)
3-7%
28
how many ppl will be affected by a genetic disease including multifactorial?
abt 60%
29
what are some examples of multifactorial diseases?
hypertension, rheumatoid arthritis, psychoses, and atherosclerosis
30
mtDNA
maternally inherited, circular, no introns
31
displacement loop (D loop)
triple stranded region of mtDNA forms a loop due to short strand called 7S DNA, contains mtDNA control region (promoter)
32
what is the result of mutations in mitochondrial genes, MT-TL1, MT-TK, or MT-TE, by reducing tRNA activities
MIDD - maternally inherited diabetes and deafness, 1% of diabetics
33
T or F: introns are spliced out of mRNA AFTER leaving the nucleus
F
34
SINEs and LINEs
-repetitive DNA segments
-Dispersed throughout genome
-makes up 45% of human genome
35
reference sequence
The base sequence that is accepted as the standard sequence for a particular species, against which all others are compared, represents the nucleotides the majority of individuals have in a sequence
36
roughly how many protein coding genes do we have?
20,000
37
"read-through" transcription
leads to conjoined genes, two genes that are very close together are read as a single transcript??
38
conjoined genes
- a gene, which gives rise to transcripts by combining at least part of one exon from each of two or more distinct known (parent) genes which lie on the same chromosome, are in the same orientation, and often (95%) translate independently into different proteins
39
what part of the human genome is useful for forensic identification, gene mapping, and sequencing in cancers to predict clinical outcome? why?
min/microsatellite DNA, they vary in length in each individual
40
4 levels of DNA packaging
1. DNA wound around 8 histones to form nucleosome
2. nucleosomes form helical solenoid
3. chromatin loops
4. chromosomes
41
what portion of oocytes contain an extra or missing chromosome?
1/4
42
what is the leading cause of pregnancy loss?
chromosomal abnormalities
43
Nondisjunction and the probabilities of abnormalities in m1 or m2
Error in meiosis in which homologous chromosomes fail to separate. in m1 = 100%, m2 = 50%
44
rearrangments
InDels, translocations, isochromosome
45
FISH
- Fluorescently labeled gene or locus-specific ssDNA probe to hybridize with chromosomes
- Need to know which mutation you are looking for to design proper probe
46
in human cells, genetic information are encoded in
mtDNA and nuclear DNA
47
trisomy 18
Edwards syndrome
48
trisomy 21
Down Syndrome
49
trisomy 13
Patau syndrome
50
Turner Syndrome
A chromosomal disorder in females in which either an X chromosome is missing or part of one X chromosome is deleted, caused by isochromosomes
51
What is a downside to Ideographs when looking for chromosomal abnormalities?
- Can't see homologous chromosomes and therefore won't detect any duplication errors
52
CGH technique
- Fix chroms at metaphase
- Stain control and test genomes different colours
- Denature DNA and mix samples
- Hybridize DNA and observe ratio of colours
53
aCGH technique
- Fix chroms at metaphase
- Isolate DNA fragments
- Stain control and test fragments different colours
- Denature DNA and mix samples
- Hybridize DNA and observe ratio of colours in a microarray containing BAC clones or oligonucleotides
54
what is the aim of karyotyping?
to determine abnormal chromosome numbers (from defective duplication or segregation) or structures (caused by rearrangments)
55
interstitial deletion vs terminal deletion
terminal occurs at the tip, interstitial occurs within the chrom
56
which kind of structural chromosomal abnormality results in the loss of all genes that code for protein synthesis machinery?
Robertsonian translocation
57
BAC
bacterial artificial chromosomes, extract DNA, use EcoRI to cut into fragments, clone fragments into vectors, transfer into bacterial cells and allow to grow and increase concentration of DNA of interest
58
structural abnormalities are present in how many newborns?
1/375
59
clastogens
chromosome breaking agents, ex: ionizing radiation, some viral infections, chemicals
60
Presence of ? distinguishes eukaryotes from prokaryotes.
introns
61
Genes that code for protein synthesis machinery are in?
the stalk
62
Cells are generally arrested at which stage of the cell cycle for use in routine karyotyping?
metaphase
63
the development of BACs facilitated which processes?
- development of aCGH (array CGH)
- human genome project
64
what method cannot be used to detect balanced translocations?
CGH
65
there are only 3 non-mosaic disorders that allow for post-natal survival, they are which? why?
- trisomy 21, 18, 13
- due to amount of protein coding genes, these 3 chroms are relatively small
66
most common prenatal trisomy
trisomy 16
67
incidence of trisomy 21 at live birth?
1/850
68
incidence of trisomy 18 at live birth?
1/6-8000
69
incidence of trisomy 13 at live birth?
1 in 12,000-20,000
70
Microcephaly, sloping forehead, characteristic fist clench, rocker-bottom feet, polydactyly
trisomy 13
71
Hypertonia, prenatal growth deficiency, characteristic fist clench, rocker-bottom feet
trisomy 18
72
Hypotonia, short stature, loose skin on nape, palmar crease, clinodactyly
trisomy 21
73
which genetic disorder results in abt 20-25% of fetuses surviving to birth?
Down syndrome (tri 21)
74
what is the primary cause of trisomy 21?
meiotic nondisjunction during maternal meiosis - extra chrom 21 - 75% in M1
75
what is the fatality rate for babies with trisomy 13 within 1st month of life? what is their expectancy for live birth?
50%
live birth = >5%
76
similar to trisomy 21, tri 13 is most commonly caused by?
nondisjunction of meiosis 1
77
20% of the cases of what are caused by unbalanced translocation?
trisomy 13
78
which genetic disorder commonly shows clenched fists, rocker bottom feet and hypertonia phenotypes?
trisomy 18 (Edwards)
79
what is nuchal translucency indicative of?
trisomies 21, 13, 18
80
what is the fastest and most commonly used prenatal diagnostic test?
rapid aneuploidy detection (2 days turnaround time)
81
how are chromosomes ordered?
by size (largest to smallest)
82
What are the odds of Down Syndrome diagnosis in the next child of a male with normal chroms and a female with one isochromosome (Robertsonian) of 21?
100%
83
what is the underlying mechanism and consequences of abnormal chrom segregation?
- mechanism = nondisjunction
consequences = aneuploidy (missing or extra chrom)
84
what is the underlying mechanism and consequences of recurrent chrom syndromes?
mechanism = Recombination at segmental duplications
consequences = Duplication/deletion syndromes and copy number variation
85
multifactorial diseases account for approximately how many congenital malformations (birth defects)?
half
86
what can be useful to sequencing in cancer patients to predict a clinical outcome?
microsatellites, their stability can predict how patient responds to treatments (like chemo and radiation)
87
during what stage of mitosis is DNA duplicated?
S phase
88
at the end of G2 the cell has ?
all the necessary proteins to divide
89
in a karyogram, light and dark regions are?
light regions = Euchromatin (less condensed, gene rich)
dark regions = Heterochromatin (highly condensed)
90
primary reason InDels happen?
shuffling of DNA in meiosis
91
G/C/R/Q and prometaphase banding are all types of?
karyotyping methods
92
duplication of all or a portion of chromosome 12p leads to ?? in which patients show characteristic craniofacial features, mental retardation, and a range of other birth defects likely to be related to trisomy or tetrasomy for specific genes present in the duplicated region
Pallister-Killian syndrome
93
what type of unbalanced rearrangement results in partial trisomy and partial monosomy? what's one syndrome this may cause?
isochromosome, Turner syndrome
94
what are the 2 possibles ways isochromosomes are formed?
mis-division through centromere (short p arms break off and 2 long q arms stay together)
defective meiotic crossover
95
3 types of translocations?
reciprocal, Robertsonian, insertion
96
para vs pericentric inversion
para = within same arm of chrom, both breaks in one arm
peri = abt the centromere, a break in each arm
97
Most common cause of mosaicism in Down syndrome trisomy? are those who carried a mosaic child at a greater or smaller risk of reoccurence?
a trisomic conception followed by loss of the extra chromosome during mitosis in some embryonic cells, carriers at greater risk of reoccurrence
98
