Midterm 1 Flashcards
(144 cards)
1
Q
What are the three levels of impact that genetics can have on individual diseases?
A
- Entirely Causative: Single gene disorders and chromosomal disorders are solely responsible for this disease. Ex. Down Syndrome
- Major Role: Genes play a major role in the appearance of the disease. Ex. BRCA1 causing ovarian cancer
- Minor Role: Multifactor models. Ex. Spina Bifida
2
Q
What are the frequencies of chromosomal genetic disease?
A
1.8/1000 by age 5
2/1000 by age 25
3.8/1000 throughout their entire life
3
Q
What are the frequencies of single gene genetic disease?
A
3.6/1000 by age 5
16.4/1000 by age 25
20/1000 throughout their entire life
4
Q
What are the frequencies of multifactorial genetic disease?
A
51.8/1000 by age 5
616.4/1000 by age 25
670.2/1000 throughout their entire life
5
Q
What fraction of persons in the population will be found to have a genetic disorder?
A
3% - 7%
6
Q
What is the most common type of genetic disorder in both children and adults?
A
Multifactorial disorders.
7
Q
What fraction of the population will be affected by genetic disease?
A
60%
8
Q
Multifactorial disorders are believed to account for approximately how much of all congenital malformations?
A
1/2
9
Q
What are the processes of clinical genetics?
A
- Diagnosis
- Prognosis
- Management
- Risk assessment/counselling
- Reproductive options
- Support
10
Q
What is the greatest growth area for genomic medicine?
A
Diagnosis
To be able to identify individuals with genetic predispositions to conditions such as cancer, heart disease, stroke, etc. and to be able to do primary prevention
11
Q
What are the three types of primary prevention?
A
- Targeted risk reduction
- Early use of medical therapy
- Gene therapy
12
Q
What is a gene?
A
The sequence of DNA that will be transcribed and translated into a protein
13
Q
What is the process of transcription?
A
Creating RNA from DNA
14
Q
What is the process of translation?
A
Creating a protein from RNA
15
Q
What is a gene product?
A
The protein that is made using the DNA sequence that makes up the gene.
16
Q
What is splicing?
A
When the introns of an RNA strand are removed
17
Q
What are the names of the two DNA strands during transcription and splicing, and how can they be identified?
A
The 5’ - 3’ end is the coding strand because that’s what’s being created by the RNA.
The 3’ - 5’ end is the template strand because that’s what’s being used to create the RNA strand.
18
Q
When the RNA is finished transcribing, what is it made up of and what part is removed?
A
Introns and Exons. Introns are removed.
19
Q
Where do replication, transcription, and translation occur?
A
Replication and transcription occur in the nucleus of the cell, translation occurs in the cytoplasm.
20
Q
What are the parts of a pre-mRNA strand?
A
The 5’ cap (m7G cap, which is a modified guanine), the 5’ UTR (untranslated region), exons and introns, the 3’ UTR, and the Poly A Tail (50-250 adenine nucleotides)
21
Q
What is polyadenylation?
A
The addition of a poly A tail to the RNA transcript.
22
Q
How many pairs and chromosomes does the average person have?
A
46 chromosomes, 23 pairs.
23
Q
How many autosomes does the average person have? What are the chromosomes that aren’t autosomes?
A
22 pairs of autosomes, 44 autosomes. 1 pair of sex chromosomes, 2 sex chromosomes
24
Q
What is mtDNA or mDNA?
A
Mitochondrial DNA.
It’s circular and doesn’t have introns.
It’s maternally inherited.
It encodes 37 genes
It has its own specific transcription and translation
It has 16.5 k base pairs
It creates 13 proteins
25
What is the structure of the Mitochondrial Genome?
It has heavy and light strands
It has a displacement loop, or a D-loop, which is triple stranded because of a short third strand called 7S DNA
The D-loop contains the mtDNA control region with the promoter
mtDNA replication is variable between cells
There are between 1,000 and 10,000 mtDNA copies within the inner matrix in a cell
Ooctyes contain 100,000 mtDNA copies
26
What is MIDD?
Maternally Inherited Diabetes and Deafness.
1% of diabetic patients have it
It's most common in the Japanese population
It's a mutation in the mitochondrial genes
It's caused by the reduction of tRNA activities.
27
What is tRNA?
Transfer RNA. It moves amino acids to ribosomes to be linked into proteins.
28
What is the Human Genome Project?
An international, collaborative research program aimed to map and understand all the genes (or the entire genome) of human beings. It began in 1990 and ended in 2003.
29
What is one of the attributes used to distinguish eukaryotes from prokaryotes?
The intron-exon structure of genes. Introns form the major portion of most eukaryotic genes. Introns are spliced out of the mRNA before it leaves the nucleus.
30
How many total genes and pseudogenes are there in the human genome?
54,000 - 58,000
31
How many protein-coding transcripts are there in the human genome?
~20,000
32
How many non-coding transcripts are there in the human genome?
17,000 - 23,000
33
How many pseudogenes are there in the human genome?
14,000 - 16,000
34
What is a conjoined gene?
A gene that creates transcripts by combining part of one exon from one gene and part of another exon from another gene from the same chromosome to create independent proteins
35
What are the three types of DNA and how much of all DNA is made up by each type?
Single-copy DNA, which makes up 45%.
Dispersed repetitive DNA, which makes up 45% and is a type of repetitive DNA.
Satellite DNA, which makes up 10% and is also a type of repetitive DNA.
36
What are the three types of Satellite DNA?
1. Alpha Satellite which is a 171 base pair sequence that can repeat extending to several million base pairs or longer and is near the centromeres.
2. Minisatellites, which are 11 base pairs long and are made up of tandem repeats. Can repeat up to a few thousand base pairs
3. Microsatellites, which are 1 - 10 base pair sequences with a total repetition length of less than a few hundred base pairs.
37
What makes minisatellites and microsatellites of special interest in human genetics?
They vary in length among individuals so they can be very useful in forensic identification and gene mapping.
38
What are the three types of dispersed repetitive DNA families?
1. SINE (short interspersed elements) family, which makes up 10% of the genome, and where each member is ~300 base pairs in length
2. LINE (long interspersed nuclear element or L1) family, which makes up 20% of the genome, and where each member can be up to 6 k base pairs in length
3. Segmental Duplication family, which makes up a little more than 5% of the genome, and where each member can span hundreds of thousands of base pairs
39
How are there so many SINE and LINE sequences in the human genome?
Some of them are able to create copies of themselves which can be inserted into other parts of the genome. Sometimes this interrupts protein-coding genes and causes genetic disease.
40
How many levels of DNA packaging are there in a chromosome and what are the levels?
4.
- The DNA is wound around histone protein cores which contain 8 histones to form a nucleosome
- Nucleosomes form a helical solenoid, and each turn of the solenoid includes about six nucleosomes
- The solenoids are organized into chromatin loops of about 100,000 base pairs of DNA
- The chromatin loops make up chromosomes.
41
What is mitosis?
The process of somatic cell division
42
What are the stages of mitosis and how long do they last?
G1 (10 - 12 hours)
S (6 - 8 hours)
G2 (2 - 4 hours)
M (negligible)
43
What are the phases of mitosis?
1. Interphase: the chromatin is floating freely
2. Prophase: the chromatin condenses with chromosome condensation and centrosomes appear
3. Prometaphase: the microtubules form
4. Metaphase: the chromosomes are in the middle of the microtubules
5. Anaphase: the chromosomes are pulled apart, half of each going to one side
6. Telophase: chromosome segregation begins, the cell is splitting and cytokinesis takes place before chromosome decondensation happens and we are back and 1
44
What are the components of a chromosome?
Telomere: the very end of the arms
Short (p) Arm: the shorter arm
Centromere: the primary constriction site where the sister chromatids attach
Long (q) Arm: the longer arm
Chromatid: one half of the chromosome that is attached to another chromatid at the centromere
45
What is meant by ploidy?
The number of different copies of each chromosome preset in a cell
Human somatic cells are diploid (2n), meaning there are two copies of each chromosomes per cell
46
What is the ploidy of human somatic cells and human gametes?
Somatic cells are 2n, diploid.
Gametes are n, haploid.
47
What is meant by c?
c refers to the number of chromatids in a cell.
48
What would a cell look like if it was 1n 1c?
It would have one single chromosome (haploid) that is unreplicated and has only one chromatid
49
What would a cell look like if it was 2n 2c?
It would have two homolog unreplicated chromosomes (diploid), each only one chromatid but totalling two chromatids
50
What would a cell look like if it was 1n 2c?
It would have one single chromosome (haploid) in which the DNA has been duplicated and there are two chromatids
51
What would a cell look like if it was 2n 4c?
It would have two homolog chromosomes (diploid) each consisting of two sister chromatids, equalling four in total
52
What is meiosis?
The process of gamete cell division
53
What are the four genetic consequences of meiosis?
1. Shuffling of the genetic materials by recombination
2. Additional shuffling of the genetic material by random assortment of the homologous chromosomes
3. Reduction of the chromosome number from diploid to haploid
4. Segregation of alleles
54
In humans, where is genetic information encoded?
mtDNA and nuclear DNA
55
True or False: most of the genomic DNAs are repetitive DNA sequences?
True.
56
True or False: Not all chromosomes have a short arm and long arm, some have equal length arms.
False. There is a short and a long.
57
When is the best time during mitosis to visualize the human karyotype?
Chromosome condensation
58
What is meiotic nondisjunction and where can it occur?
The homologous chromosomes or the sister chromatids of a chromosome fail to separate from one another and travel to the opposite poles, resulting in cells that do not have the normal number of chromosomes.
It can occur at the first phase of splitting or the second phase of splitting.
The first phase would result in two gametes with one extra chromatid, and two gametes with one fewer chromatid.
The second phase would result in two gametes with the usual number of chromatids, one gamete with one extra chromatid, and one gamete with one fewer chromatid.
59
True or False: all mutations are bad.
False, mutations are important for variability and evolution. Lactose tolerance in humans is a mutation at a site 14,000 nucleotides away from the lactase gene.
60
What is the stalk of a chromosome and what do they contain?
They're the thin ends of a acrocentric chromosome end and they contain ribosomal DNA genes and they form the nucleolus during interphase
61
What is the satellite of a chromosome?
The non coding region of a acrocentric chromosome.
62
What are the three types of chromosomes categorized based on centromeres?
Metacentric, when the centromere is near the middle of the chromosome.
Submetacentric, when the centromere is between the middle and the telomere.
Acrocentric, when the centromere is near the telomere.
63
What is clinical cytogenetics?
The practice of medical genetics by studying structure and number of chromosomes to identify chromosome abnormalities and disorders
64
What is aneuploidy?
One or more missing or extra chromosomes.
Ex. Trisomy 47, one extra chromosome.
65
What is polyploidy?
Having more than two complete sets of chromosomes
66
What is triploidy?
A condition where you have an extra set of chromosomes.
67
What is trisomy?
A condition where you have an extra chromosome
68
Chromosomal abnormalities are the leading cause of what?
Pregnancy loss
69
What percentage of pregnancies are afflicted with chromosomal abnormalities and what percentage of those don't make it to term?
10-20%
95%
70
What percentage of oocytes have an extra or missing chromosome?
20-25%
71
What are the five clinical indications for chromosomal disorders?
1. Problems with early growth and development
2. Stillbirths and neonatal deaths
3. Fertility issues
4. Family history
5. Pregnancy in people of advanced age
72
At what age does a pregnant person have an increased risk of chromosome abnormalities in their fetus?
35 years old
73
What are the seven cytogenetic technologies used to find chromosomal abnormalities?
1. Routine cytogenetic analysis
2. Q Banding
3. R Banding
4. Special procedures
5. FISH
6. Molecular technologies
7. CGH and microarray
74
What is karyotyping?
Displaying all the chromosomes of a person and ordering them
75
What are the goals of karyotyping?
To determine abnormal chromosomal numbers caused by defective duplication and or segregation
to determine abnormal chromosomal structures caused by rearrangements (insertion, deletion, translocation)
76
What is the difference between interstitial deletion and terminal deletion?
Interstitial deletion is the deletion of a part of the chromosome in the middle between the centromere and the telomere.
Terminal deletion includes the deletion of the telomere
77
What is Robertsonian translocation?
When two acrocentric chromosomes fuse at the centromeres with the loss of their short arms
78
What is the process of karyotyping?
1. Take a blood sample
2. Use heparin to get the white blood cells
3. Grow them in a culture
4. Use colcemid to arrest the cells at metaphase
5. Use a hypotonic solution to fix them and stain them
6. Obtain your chromosome spread
79
What is G-banding?
Staining chromosomes with Giesma stains. It creates light GC rich regions and dark AT rich regions, which shows the banding. This is the most common method for cytogenetic analysis.
80
In karyotyping, how are they able to identify which chromosome is which?
Using G banding, which will create a predictable pattern on the chromosomes, and by using their length, which are well documented for each chromosome
81
What is Q Banding?
Staining with quinacrine mustard.
It's used to detect heteromorphisms
82
What is a heteromorphism?
A morphological variant of a chromosome. A homologous chromosome pair which are not morphologically identical
83
What is R Banding?
Reverse banding. The results are the reversed band colours for G and Q banding. The specimen is heated before staining occurs. It's used to analyze the distal ends of chromosomes which stain poorly with G and Q banding. It's the standard method in Europe.
84
What is C Banding?
Uses xylene substitutes for staining centromeric regions and regions containing constitutive heterochromatin.
85
What is constitutive heterochromatin?
A type of condensed chromatin that lies near the centromere
86
What is prometaphase banding?
Uses G or R banding methods to stain chromosomes that are at the early mitotic stage prometaphase. Used to identify subtle structural abnormalities of chromosomes. It increases the resolution or number of visible bands from 300 to anywhere from 450 to 800. They become longer and skinnier.
87
What are the types of karyotyping?
G banding
Q banding
R banding
C banding
Prometaphase banding
88
What type of banding would you use if you wanted to get a standard overview of one's chromosomes?
G banding
89
What type of banding would you use if you wanted to check for chromosomal heteromorphisms?
Q banding
90
What type of banding would you use if you wanted to view the distal ends of a chromosome?
R banding
91
What type of banding would you use if you wanted to see the centromeric regions of a chromosome?
C banding
92
What type of banding would you use if you wanted to view the constitutive heterochromatin regions of a chromosome?
C banding
93
What type of banding would you use if you wanted to view a chromosome in higher resolution, with more detailed bands?
Prometaphase banding using G or R banding
94
What is FISH?
Fluorescence In Situ Hybridization.
The use of fluorescent labelled ssDNA probes to hybridize with chromosomes immobilized on microscope slides to identify chromosomal aberrations.
Gene specific or locus specific probes that can be used to detect chromosomes
95
What is Smith-Magenis Syndrome?
a 17p deletion that causes a broad forehead and a flat face
96
What is spectral karyotyping?
SKY.
A technique where all 24 probes of the human chromosomes are combined and used for FISH on metaphase chromosomes. Each chromosome-specific probe emits its own signal and therefore, abnormal chromosomes consisting of pieces of different chromosomes can be identified
97
What is it called if a pair of chromosomes both consist of half chromosome 2 and half chromosome 6?
Rearrangement
98
What is amplification?
An increase in the number of copies of a gene sequences
99
What are the steps in the process of amplification of DNA fragments?
1. You have a human cell
2. You collect the DNA from it
3. The sequences of interest is marked
4. Each fragment is cut by PCR
5. You use restriction enzyme digestion to have a mixture of restriction fragments
6. There's a library of different fragments
7. You isolate and replicate the clone with a sequence of interest
100
What is a plasmid?
A extra chromosomal DNA molecule found in bacteria and can be replicated independently from the microorganism's own chromosomes
101
What is a vector?
A plasmid that has been engineered for application in molecular biology
102
What are the steps in molecular cloning?
1. You have a plasmid that an enzyme cuts to create complimentary sequences
2. The sticky ends are created on human DNA
3. The human DNA is added to the plasmid using DNA ligase
4. The resulting vector is inserted into bacterial cells through heat shock and ice, or electrical currents
5. Antibody resistance is created
6. The plasmids are isolated
103
What is a DNA library?
A collection of clones, each of which carries a vector molecule into which a different fragment of DNA derived from the total DNA or RNA is inserted. They only contain exons.
104
What is a genomic library?
A collection of total genomic DNA from an organism. They only contain exons.
105
What is a genomic DNA?
a complete gene or a fragment of a gene, including introns and exons
106
What is a cDNA library?
A combination of cDNA fragments inserted into a collection of host cells, which together constitute the "transcriptome" of the organism.
They only contain exons.
107
What is cDNA?
Complementary DNA. A coding DNA fragment synthesized from a mRNA template using reverse transcription
108
What is nucleic acid hybridization?
A process of establishing a sequence-specific interaction between 2 or more complementary strands of nucleic acids into a single complex.
Two single stranded DNAs become a renatured, double stranded DNA.
109
What process is essentially denaturation?
FISH.
110
How can hybridization and denaturation indicate if two genomes are identical?
If you stain one fragment one colour, and the other a different colour, then you denature them and hybridize them, you can see what colour is created. If they're the same, there will be some DNA that is half colour A and half colour B, creating a third colour C. If they aren't the same, you will only have the two initial colours.
111
What is CGH?
Comparative Genome Hybridization.
It's used to determine the number of differences between two distinct DNA samples.
It's useful for detecting deletions and duplications.
112
Why is CGH better than routine cytogenetic analysis to detect small mutations like < 1 M base pairs deletions and duplications?
Because they're too small to be visible using banding.
113
If you colour patient DNA blue, and control DNA black, what colour would indicate the same amount of DNA from both samples using CGH?
Grey, or a combination of blue and black. A middle colour.
114
If you colour patient DNA blue, and control DNA black, what colour would indicate a duplicated gene or region in the patient DNA using CGH?
Blue.
115
If you colour patient DNA blue, and control DNA black, what colour would indicate a deleted gene or region in the patient DNA using CGH?
Black
116
True or False: in CGH, you still need to culture the chromosomes.
False. You only need to collect them.
117
When would a microarray be used?
When the deletions and duplications are less than 5 - 10 M base pairs.
118
What is a DNA microarray?
A collection of microscopic DNA spotted onto a solid surface for measuring the expression levels of large numbers of gene simultaneously or to genotype multiple regions of a genome.
119
What are the methods of genomic hybridization?
1. Fluorescence In Situ Hybridization (FISH)
2. Spectral Karyotyping (SKY)
3. Comparative Genome Hybridization (CGH)
4. Microarrays
120
1 in how many newborns have a structural abnormality?
1 in 375.
121
What is the most common cause of chromosomal structural abnormality?
Structural rearrangement caused by chromosome breakage.
122
What is a clastogen?
A chromosome breaking agent. Ex. radiation, viral infections, chemicals
123
What are the two ways a structural rearrangement can be present in a person?
In all their cells or in a mosaic form.
124
What is mosaicism?
A mutation occurs in one cell of the developing embryo so only the child cells of that cell have the mutation while the others don't. So the organism is a mosaic of mutated and nonmutated cells.
125
What is unbalanced rearrangement resulting in duplication or deletion and what are the results of that?
It's when rearrangement occurs but the chromosomes do not line up properly. This can lead to duplication of a gene or deletion of a gene.
126
What is haploinsufficiency?
The inability of a single copy of genes to carry out the function normally performed by two copies.
127
There is a set of chromosomes where one chromosome is missing a gene. The other matching chromosome does have that gene, but the function of the gene is unable to be properly carried out. What is this called?
Haploinsufficiency.
128
What is Pallister-Killian syndrome?
The duplication of all or a portion of chromosome 12p
129
What is a marker chromosome?
An additional chromosome that is in a ring shape. It's naturally occurring but very rare. They're very small and difficult to identify.
Despite not having ends, it's not a deletion because there's extra information.
130
What is an isochromosome?
A chromosome in which one arm is missing (partial monosomy) and the other is duplicated (partial trisomy) in a mirror image fashion.
131
What is Turner syndrome?
Having an isochromosome X chromosome
132
What are the two ways in which an isochromosome can come to be?
Misdivision through the centromere, where instead of splitting up by chromatids at the centromere, the chromosome splits so the short arms are one chromatid and the long arms are the other.
Or defective meiotic crossover, where the crossover spot fuses and creates two normal chromosomes, one defunct acentric chromosome, and one dicentric isochromosome.
133
What is a dicentric chromatid?
An isochromosome that has two centromeres. It comes around by defective meiotic crossover.
134
What is a pseudodicentric chromosome?
Dicentric chromosomes that are mitotically stable due to one of the two centromeres being inactive, or both centromeres always coordinate their movement to one of the mitotic poles during segregation
135
What are the possible outcomes of unbalanced rearrangements?
Duplication of parts of a chromosome (partial trisomy).
Deletion of parts of a chromosome (partial monosomy).
Marker and ring chromosomes.
Isochromosomes.
Dicentric chromosomes and pseudodicentric chromosomes.
Acentric chromosomes.
136
How can one detect deletion or duplication?
FISH and microarrays
137
What are the possible outcomes of balanced rearrangements?
Inversions (paracentric, pericentric).
Translocations.
138
What are inversions?
A chromosomal inversion occurs when a single chromosome undergoes two breaks and is reconstituted with the segment between the break inverted. So a chunk of the chromosome is spun around.
139
What are the two types of chromosomal inversions?
Paracentric. It does not include the centromere. Both breaks are in one arm. Can be identified with banding or FISH probes.
Pericentric. It does include the centromere. There is a break in each arm. Can be identified with C banding.
140
What are translocations in the context of balanced rearrangement abnormalities?
A chromosomal translocation involves the exchange of chromosome segments between two non-homologous chromosomes.
141
What are the two types of trans locations in the context of balanced rearrangement abnormalities?
Reciprocal translocations, also called an even swap. The total genetic material remains exactly the same. The total chromosome number is unchanged. Only happens on metacentric and submetacentric chromosomes.
Robertsonian translocations, a deletion of short arms on acrocentric chromosomes. One less chromosome.
142
True or False: introns are located between the promoter and the first exon of a gene?
False. Sometimes exons are first.
143
True or False: introns are spliced out from noncoding mRNA molecules before translation.
Introns are noncoding mRNA segments.
144
True or False: intronic region of mRNA is stabilized by a modified nucleotide m7G cap before translation.
The intronic regions are removed, so we wouldn't want to stabilize them.
