Genomics Exam 1 Material Flashcards
(177 cards)
1
Q
Genes have ____________ ____________ such as promoters and enhancers.
A
regulatory domains
2
Q
DNA is (translated/transcribed) into RNA.
A
transcribed
3
Q
Spliced RNA is ___________, or the introns are removed.
A
matured
4
Q
(transcription/translation) occurs when RNA is made into protein by ribosomes.
A
translation
5
Q
What is the process where DNA is used as a template to synthesize RNA?
A
transcription
6
Q
RNA is the only known molecule to function in what two processes?
A
storage and transmission of genetic information and catalysis
7
Q
Uracil pairs with which nitrogen base in RNA?
A
adenine
8
Q
Replication uses (both strands/a single strand) as a template.
A
both strands
9
Q
Which process—replication or transcription—uses a primer?
A
replication
10
Q
What is the main enzyme in the process of replication?
A
DNA polymerase
11
Q
What is the main enzyme in the process of transcription?
A
RNA polymerase
12
Q
What is the final product of replication?
A
dsDNA
13
Q
What is the final product of transcription?
A
ssRNA
14
Q
True or False: Proofreading occurs in both replication and transcription.
A
true
15
Q
What is a codon?
A
three letter code for an amino acid
16
Q
What are sense codons?
A
codons that are degenerate (many codons code for the same AA)
17
Q
What are nonsense codons?
A
codons that code for a stop codon (there are 3 of them)
18
Q
Translation starts at the codon _______.
A
AUG
19
Q
Codons are recognized by which molecules?
A
tRNA
20
Q
What links all the amino acids together?
A
the ribosome
21
Q
What is the primary structure of a protein?
A
sequence of amino acids
22
Q
What is the secondary structure of a protein?
A
structure of AA that includes the alpha helix and beta-pleated sheet
23
Q
What is the tertiary structure of a protein?
A
3D shape of a polypeptide due to interactions of the R groups of the amino acids
24
Q
What is the quaternary structure of a protein?
A
the shape resulting from the association of two or more polypeptide subunits
25
What usually occurs for signaling pathways to start?
phosphorylation of molecules
26
What does acetylation of DNA and histones cause?
nucleosomes to loosen and spread apart; increases access to DNA and makes it more likely to be expressed
27
What does methylation of DNA do?
makes genes less likely to be expressed.
28
What is glycosylation?
addition of carbohydrate groups to the membrane that allows for cell signaling
29
What is ubiquitylation?
the targeting of molecules to be destroyed
30
What does degradation refer to?
the targeting of molecules to be destroyed
31
What is a microsatellite?
a short, specific and repeating sequence of nucleotides (2-5 base pair motif repeated)
32
What are repetitive elements in our genome?
they are hypermutable, meaning they are very prone to mutations
33
What are LINES?
long interspersed nuclear elements (an interspersed repeat)
34
What are SINES?
short interspersed nuclear elements (an interspersed repeat)
35
What are LTR retrotransposons?
a type of retrotransposon that is derived from a virus and has long terminal repeats
36
What can integrate into the genome and disrupt gene coding sequence or affect gene regulation/transcription?
interspersed repeats (LINES, SINES, LTR retrotransposons)
37
Is the central dogma always followed?
no
38
True/False: Mutations located in introns are never of any consequence.
false
39
What is aneuploidy?
an abnormal number of chromosomes; can be trisomy, monosomy
40
What is a mutation?
any change in the arrangement of, or nucleotide sequence, in DNA
41
What is a substitution mutation?
one nucleotide replaces another; could be synonymous (same codon produced), missense (changes AA), or nonsense (stop codon)
42
What is an insertion mutation?
mutation that could cause the addition of an AA or a frameshift mutation
43
What is a deletion mutation?
mutation that could cause the loss of an AA or a frameshift mutation
44
What are hot spots?
regions with particularly high rates of mutation
45
What is a lethal mutation?
a mutation that severely impairs function and results in death of the organism
46
What is a neutral mutation?
a mutation that has no impact on form or function
47
What is a polymorphism?
a neutral mutation that reaches a frequency of 1% in the population
48
What is haploinsufficiency?
occurs when a gene doesn't produce enough protein (reduced or missing)
49
What is loss of function?
the phenomenon in which a person has only a single functional copy of a gene, and that single functional copy does not produce a normal phenotype (i.e. 50% not sufficient)
50
What is gain of function?
occurs when a novel protein product is produced, or there is over-expression/inappropriate expression of a gene's product
51
What is a dominant negative mutation?
refers to how one allele is enough to disrupt phenotype (e.g. in gains of function)
52
What is DCM (dilated cardiomyopathy)?
also called round heart disease in turkeys; sudden death is caused by cardiac arrest & onset is within the first few weeks of life
53
What causes DCM in turkeys?
a deletion in intron 7 that causes skipping of exon 8 in the cardiac troponin T gene
54
What negatively affects cardiac muscle contractility in turkeys with DCM?
incorporation of the mutant troponin T into the myofibrils
55
What does N refer to?
the number of chromosomes found in gametes
56
What does 2N (diploid) refer to?
the number of chromosomes found in somatic cells (e.g. 1N, 2N, 4N)
57
What are autosomes?
non-sex chromosomes
58
What are sex chromosomes?
typically X and Y (or W & Z in birds)
59
Which sex is homogametic XX in mammals?
females
60
Which sex is homogametic ZZ in birds?
males
61
What is the M phase?
The phase of the cell cycle that includes mitosis and cytokinesis
62
What is the G1 phase?
stage of interphase in which cell grows and performs its normal functions
63
What is the S phase?
the phase of the cell cycle where DNA is replicated
64
What is the G2 phase?
The phase of the cell cycle that involves growth and preparation for mitosis
65
What is interphase?
part of the cell cycle that includes G1, S, and G2
66
What is a sister chromatid?
each arrow is pointing to one sister chromatid
67
What is a centromere?
area where the chromatids of a chromosome are attached
68
What is the p arm?
short arm of chromosome
69
What is the q arm?
long arm of chromosome
70
What are homologues?
chromosomes that are given the same number, but are of opposite parental origin
71
What are metacentric chromosomes?
type of chromosomes in which the centromere is in the middle
72
What are submetacentric chromosomes?
type of chromosomes in which the centromere is slightly off center
73
What are acrocentric chromosomes?
type of chromosomes in which the centromere is located at the terminal end
74
What is a karyotype?
a display of the chromosome pairs of a cell arranged by increasing size and shape
75
What does BTA4 represent?
bovine chromosome number 4
76
What does CFA7 represent?
canine chromosome number 7
77
What does HSA8 represent?
human chromosome number 8
78
What does ECA2 represent?
horse chromosome number 2
79
What does FCA1 represent?
cat chromosome number 1
80
What does SSC9 represent?
pig chromosome number 9
81
What is crossing over?
process in which homologous chromosomes exchange portions of their chromatids during meiosis; gives us a mixture of traits
82
What is haploid?
chromosome number (n) in a gamete = 1N
83
What is diploid?
chromosome number (n) in a zygote = 2N
84
What is a gene?
basic unit of inheritance
85
What is an allele?
form/version of a gene
86
What is homozygous?
both alleles are the same (AA or aa)
87
What is heterozygous?
both alleles are different (Aa)
88
What is hemizygous?
only 1 allele is possible (e.g. allele on X or Y chromosome in males)
89
True/False: There are only 2 alleles per gene in mammals.
false
90
What is dominant?
phenotype is seen in heterozygotes
91
What is recessive?
phenotype is only expressed in homozygotes
92
What is incomplete dominance?
pattern of inheritance in which there is a blended phenotype, a mix between the two alleles
93
What is codominance?
a condition in which both alleles for a gene are fully expressed
94
What is genotype?
genetic constitution or alleles present
95
What is phenotype?
physical manifestation of a genotype + environment
96
What is incomplete penetrance?
individual that has a gene but doesn't express the phenotype
97
What is variable expressivity?
refers to how individuals with the same genotype can have related phenotypes that vary in intensity
98
What contributes to genetic variance?
dominance deviations, epistatic interactions, and the environment
99
What does the law of segregation state?
each individual possesses two genes for a particular trait, but only one of these genes is transmitted to the offspring
100
What does the law of independent assortment state?
genes can be transmitted independently from one another
101
The closer the two genes are located on a chromosome, the (less/more) likely they will be inherited together.
more
102
True/False: Most disease traits are rare in the general population.
true
103
True/False: Members of the same breed or family have less gene variants in common than members of different breeds or families.
false
104
What phenotype is a dominant trait in beef cattle of European ancestry?
polled
105
What is von Willebrand's disease?
inherited bleeding disorder common amongst dogs; caused by an absent or defective vWF clotting factor
106
What type of vWF disease indicates that the factor is functional but is only present in low amounts?
type I (vWF disease)
107
What type of vWF disease indicates that the factor is defective?
type II (vWF disease)
108
What type of vWF disease indicates that the factor is absent?
type III (vWF disease)
109
What kind of inheritance is shown in this pedigree?
autosomal recessive
110
What is inbreeding?
is often seen in pedigrees for recessive traits
111
What diagnosis test is preferred to see if a dog has von Willebrand's disease?
ELISA (but genetic testing is more accurate)
112
What autosomal recessive trait is shown here?
double muscling
113
What gene is affected to cause double muscling of an animal?
myostatin (chromosome 2)
114
What causes double muscling?
hyperplasia of the muscle cell fibers
115
What is the downside to double muscling of animals?
they have less stress tolerance, infertility and calf viability problems
116
What mutation affects Belgian Blue and Piedmontese cattle?
myostatin mutation
117
What kind of inheritance does this pedigree show?
x-linked dominant
118
What mode of inheritance is shown where affected males pass the trait to all female offspring but to none of their male offspring?
x-linked dominant
119
True/False: Affected females with an x-linked trait can pass the trait to both male and female offspring.
true
120
What is chondrodysplasia punctata?
x-linked dominant disease that causes skeletal abnormalities
121
What kind of inheritance does this pedigree show?
x-linked recessive
122
What is dwarfism?
sex-linked recessive trait in poultry that results in a smaller body frame, deficiency long bone growth, but normal fertility
123
What are the sex chromosomes for female birds?
ZW
124
What are the sex chromosomes for male birds?
ZZ
125
What is non-mendelian inheritance?
inheritance of traits that do not follow mendelian patterns of inheritance; includes multiple genes & mitochondrial genes
126
How many mitochondrial genes are there in mammals?
37
127
What is maternal inheritance?
inheritance that is passed down from the mother
128
True/False: No affected male will transmit the disease.
false
129
True/False: It isn't random.
false
130
True/False: There is a proportion of heteroplasmy.
true
131
What is homoplasmy?
the presence of only one type of mitochondrial DNA within a cell
132
What is heteroplasmy?
the presence of more than one type of mitochondrial DNA within a cell
133
What is the proportion of heteroplasmy?
10
134
What is non-Mendelian inheritance?
Inheritance of traits that do not follow Mendelian patterns; includes multiple genes and mitochondrial genes.
135
How many mitochondrial genes are there in mammals?
There are multiple mitochondrial genes in mammals.
136
Inheritance of mitochondria is only through which lines?
Maternal lines.
137
True or False: A stallion affected by a mitochondrial disease is likely to pass it on to his offspring.
False (no affected male will transmit the disease).
138
True or False: Segregation of mitochondria during mitosis and meiosis is tightly controlled.
False (it isn't).
139
How are mitochondria distributed during cell division?
Mitochondria distribute randomly between daughter cells.
140
What is homoplasmy?
A pure population of all normal mitochondrial DNA or all mutant mitochondrial DNA.
141
What is heteroplasmy?
A mixed population of normal and mutant mitochondrial DNA.
142
What does the expression of the disease phenotype depend on?
Accumulations of mutations in mitochondrial DNA and increasing proportion of mutant mitochondrial DNA.
143
How much higher is the mutation rate in mitochondrial DNA compared to nuclear DNA?
The mutation rate in mitochondrial DNA is 10-fold higher.
144
What is the effect of heteroplasmy on disease expression?
It leads to reduced penetrance, pleiotropy, and variable expressivity.
145
What is canine spongiform leukoencephalomyelopathy?
A disease affecting dogs, linked to mitochondrial mutation that leads to deficiency of electron transfer and ATP production.
146
What is liability in the context of genetic disorders?
The combined effect of genetic and environmental factors that contribute to whether an animal develops a disorder.
147
What is the threshold in genetic disorders?
A certain level of liability above which all animals will develop the disorder and below which animals will be unaffected.
148
What is hip dysplasia?
A complex disorder seen in over 82 dog breeds, highest incidence in large breeds.
149
What does multifactorial mean?
Complex disorders are often multifactorial, meaning they are due to a combination of genetic and environmental factors.
150
What is heterozygosity?
The presence of different alleles at a gene locus.
151
What are genome association studies?
Tests for association of variants with a given phenotype.
152
What does OFA stand for?
Orthopedic Foundation for Animals.
153
True or False: Clinical signs can accurately predict the severity of a dog's hip dysplasia.
False (radiographs will often look worse than what the dog is showing).
154
What is a double merle?
Breeding of a merle x merle; offspring will be at high risk of developing micropthalmia and/or deafness.
155
What is flashy in dog breeding?
Slang for a boxer with white markings; more white covering the dog may result in a higher risk of being deaf.
156
What is copper toxicosis?
A disease affecting a large percentage of the population in Bedlington terriers.
157
What is dilated cardiomyopathy?
A disease with higher prevalence in German Shepherds and Boxers; late onset and equivalent to ALS in humans.
158
What is degenerative myelopathy?
A disease with common juvenile onset in Portuguese Water Dogs; sudden death usually occurs.
159
What is progressive retinal atrophy?
Degeneration of the retina common in multiple breeds of dogs.
160
True or False: There is no gene test for hip dysplasia in dogs.
True.
161
What is collie eye anomaly?
A genetic condition affecting the eyes of collies.
162
What is SPAID?
A simple autosomal recessive disease that can be tested for at 5-6 weeks.
163
What is myostatin deficiency?
A mutation in the myostatin gene causing double muscling; prevalent in whippets.
164
What is color dilution alopecia?
A condition occurring in dogs with silver/blue coloring, especially in 'rare' silver Labradors.
165
What has shaped dogs to the desired size, shape, behavior, and temperament?
Selective breeding throughout history following the domestication of dogs.
166
True or False: Purposefully breeding dogs results in increased predictability in trait expression.
True.
167
True or False: All genetic diseases can be prevented by choosing the right sire and dam combination.
False (it can still happen!).
168
What is expressivity?
How dogs with the same mutation can manifest the trait or disease to different degrees.
169
What is epistasis?
The genetics of how one mutation can mask the effects of another.
170
What is incomplete penetrance?
Explains how a dog with the disease mutation appears to be clinically normal.
171
What is dermatomyositis?
An autoimmune disease affecting skin and muscle; occurs in Shelties and Collies.
172
What is a haplotype?
A set of genetic mutations combined to create a specific genetic profile.
173
True or False: DNA testing of dogs is highly regulated by the OFA.
False (no regulatory or oversight bodies, no industry guidelines).
174
What is hyperuricosuria?
A fixed mutation in the SLC2A9 gene causing high levels of uric acid, leading to urate stones.
175
What is Fanconi syndrome?
A late-onset kidney disorder where dogs do not reabsorb electrolytes and nutrients.
176
True or False: Breeding decisions based on a single testable gene or phenotypic test are often inappropriate.
True.
177
What should be used as a tool to apply selective pressure to produce healthier offspring?
Health screening.
