2nd half Flashcards
(186 cards)
1
Q
severe combined immunodeficiency disease (SCID)
A
Also known as bubble boy syndrome, caused by mutation in adenosine deaminase (ADA) gene. No normal response to infection. because no ADA means no other enzymes after ADA. Makes shit ton of Deoxy ATP which destroys t cells and prevents b cells from being activated
2
Q
how is gene therapy done for SCID
A
remove ADA deficient lymphocytes from scid patient, culture cells in lab, infect cells with a retrovirus that has normal ADA gene, reinfuse ADA-gene back into SCID patient. the patients need some levels of t cells
3
Q
what are the effects of gene therapy for SCID (negative and positive)
A
one patient developed immunity to gene transfer system, little to no ADA expression. no adverse effects otherwise.
4
Q
how do you get dna into cells for gene therapy, pros and cons of each
A
viral vectors (easy, fast), electroporation (breaking membrane, harmful), direct injection into blood or other tissue (depends on target, inefficient), particle bombardment (harmful), liposomes (inefficient), crispr (in the future, may have off target effect). (even voldemort doesn’t like crack pipes)
5
Q
adeno-associated virus (AAV) characteristics
A
specific chromosomal site, long term expression, nontoxic, infects dividing and nondividing cells, carries small genes. has an episome.
6
Q
adeno-associated virus (AAV) applications
A
cystic fibrosis, sickle cell disease, thalassemias, canavan disease (cindy stole talia’s candy)
7
Q
adenovirus (AV) characteristics
A
large virus, carries large genes, transient expression (not long), evokes immune response, infects dividing and nondividing cells
8
Q
adenovirus (AV) applications
A
cystic fibrosis, hereditary emphysema, (also used for otc deficiency
9
Q
herpes characteristics and applications
A
long term expression, infects neuroglia, used for brain tumors.
10
Q
retrovirus characteristics
A
stable but imprecise integration, long term expression. most types only infect dividing cells, nontoxic. integrates into the genome itself, which may cause cancer. can deliver big genes
11
Q
retrovirus applications
A
gaucher disease, hiv infection, cancers, scid (combined with adenovirus and herpes: cindy obsessively hates engineering but greatly hates computer science)
12
Q
how to make sure enough transgene will be in the right cells at the right time??
A
Ex vivo is the best, strong promoters, tissue specific promoters. insulators (prevent transgene from silencing surrounding environment, prevents enhancers from activating the wrong stuff around transgenes)
13
Q
immune responses to vector or transgene product cause what
A
reduction in transgene expression, adenovirus causes common cold, and since everyone has immunity against it, cells expressing transgene shit get deleted
14
Q
what is the problem with transgene inserting into a functional gene, consequences?
A
common for DNA to go to actively transcribed parts of genome, and could promote proto-oncogenes or tumor suppressor genes
15
Q
What is SCID X-linked mutations due to
A
deficiency in IL2 receptor gamma
16
Q
How did the gene therapy trials in france aim to remedy SCID X-linked, what are the results
A
ex vivo gene therapy of CD34+ cells (which are precursors to lymphocytes, which are the missing B and T cells). the results are that 3 of 11 got t-cell lymphoblastic leukemia, but 10 developed functional immune system
17
Q
What will happen if a transgene is put into LMO2 gene
A
it will have a ton of LMO2 protein because the transgene boosted expression rates
18
Q
Why does moving LMO increase expression
A
you probably moved it next to an enhancer
19
Q
leber congential amaurosis (LCA)
A
visual impairment in childhood, total blindness when 30-40. abnormal roving eye movements (nystagmus) and abnormal electroretinography (ERG). poor pupillary light reflexes
20
Q
what genes does LCA affect
A
5% of LCA patients have muated RPE65. You can have homozygous or compound hetero mutations. RPE65 affects phototransduction and photoreception
21
Q
how did briard dogs help us know about LCA
A
four nucleotide deletion (AAGA) makes a premature stop codon
22
Q
What vector was used for RPE65 gene therapy, how was it
A
rAAV2, adult subjects remained healthy
23
Q
What does prof nirenberg do to let blind people see
A
For people with no photoreceptor, they get optogenetic components put into retinal ganglion cells to let ganglion cells work as photoreceptors. They then wear glasses with an encoder that helps visualize for the ganglion cells, so the brain can construct an image
24
Q
incomplete dominance
A
red and white get pink
25
codominance
black and white get spots
26
additive inheritance
independently segregating loci that adds up, a special type of incomplete dominance
27
two hypothesis of quantitative traits
segregation of alleles at many loci, loci have small, equal, additive effects. quantitative trait can be explained by few genes with large additive effects
28
quantitative traits are also called
polygenic/multifactorial
29
how is familial hypercholesteraemia an example of incomplete dominance
heterozygous phenotype distinct from either homozygous phenotype to get an intermediate
30
what is qtl (quantitative trait locus)
a trait that is affected continuously by the environment and multiple genes. can be masked by environment or the genes
31
why are complex traits shaped like a normal curve
because they are the sum of various phenotypes which form small hills
32
Vp =
Vg + Ve
33
Vg =
Va + Vd + VI
34
what does broad sense variation document
how much phenotypic variation is attributable to genotypic variation
35
narrow sens variation
family specific predictability of phenotype based on parental phenotype. additive effects are the only transmissible effects
36
what doesnt h^2 tell you
whats happening in other families, what the genes are
37
How to identify a QTL
inbreed two tomatos, one big one small. you get heterozygous f1. Then breed f1 to get a bunch of combined tomatoes, determine frequency distribution in F2,genotype individuals to find markers that cosegregate with trait (eg. a marker only appears in big tomato). then use a statistical method. calculatee lod
38
lod formula
probability of linkage given the recomb rates/probaility of no linkage
39
how to determine recomb rates for lod
see what the grandparents passed down to paretns, then use that to see if the same allele formed recomb or parental for children. if 1/11: (1/11) * (10/11)^10
40
whats the lod demominator
if 11 items. (0.8)^11
41
what are RILs
recombinant inbred lines, inbred for multiple generations so you get a ladder like mosaic of paternal and maternal alleles. this allows for fine mapping of traits
42
what do you do when you find quantitative trait loci
create recombinant inbred lines, identify specific candidate genes in the QTL interval with fine mapping. NILs used to map QTL to a gene (do all the big tomatoes have gene A? do all the small tomatoes?). examine candidate gene with pcr, to see if it is really expressed in big or small plants, then check to see if the function makes sense. use genetic engineering to test candidate gene
43
what are indel mutations
insertion deletion
44
subsitution mutation
base replaced by one of other 3 bases
45
reciprocal translocation
2 nonhomologous chromosomes change places
46
transition subsitution
a to g (purine to purine) or c to t (pyrimidine to pyrimidine)
47
transversion
purine to pyrimidine or vice versa
48
backgroundrate of mutation
2-12 * 10^-6 mutations per gene per gamete
49
depurination
guanine gone (cannot be adenine)
50
deamination
cytosine changed to uracil
51
x ray mutation
deletion
52
uv light mutation
thymine dimer
53
oxidation
guanine to go, which mispairs with A
54
what do indel mutations cause
loops in dna for the loop that has extra with respect to the other
55
how to know strength of selection for a mutation
compare nonsynonymous with synonymous. neutral genes have similar rates
56
what two types of mutation change length of protein
frameshift, nonsense
57
intragenic supressor mutations
a mutation that compensates for another (check)
58
how can mutations be outside the coding sequence
disrupts splice donor and acceptor site
59
null (amorphic mutation)
mutant has the same amount of activity as if its deleted
60
hypomorphic (leaky) mutation
mutant is less severe than straight up deleting the allele
61
what makes a loss of function mutation haploinsufficient or sufficient?
threshold for wt trait
62
hypermorphic mutation
too much prtein
63
neomorphic mutation
protein with new function, or normal protein made at wrong time and place
64
what does unequal crossing over in human vision do
natural variation in r/g vision
65
alkaptonuria
phenylalanine eventually makes homogentistic acid (HA) needs an oxidase to turn it into smth else. without it, HA accumulates and you have black pee
66
how do biosynth pathways work
if there is a plus, then the compound is after the point of mutation. because if its after the mutation, it makes what the mutation is supposed to but doesn't
67
how do you get a partially yellow and purple corn
if there is wild type, it is purple. if the acentric fragment witht he dominant parts is lost, then its yellow. this is due to ac activated chromosomal breakage at ds
68
how do you get spotted corn
a ds element disrupts color gene, turning it recessive. however, ds is rebellious and randomly leaves sometimes. or you could have an ac instead of ds + ac in the color region of the DNA that jumps out
69
what is flanked by short repeats
transposed DNA
70
how much of the drosophila and human genome do TEs take up
12.5 and 34 respectfully %
71
after a p element is excised for transposons, how is the gap repaired
using a homologous chromosome. transposon will remain in original position if homologous chromosome also has it
72
What is a line
autonomous retrotranposon 1-5kb
73
What is a sine
nonautonomous retrotransposon 100-300kb
74
why dont TEs kill all of us
usually in introns. sometimes dont work because no repeats at the ends. heterochromatin prevent it.
75
what kinds of mutations could happen with TEs
unequal crossing over leading to deletions and duplications, or seeing 2 tes as one big te and yoinking that whole thing
76
how are transposable elements used in the lab
gene on a plasmid can be put into nuclei with a helper plasmid that can then be shown to express the gene. this can be done to germ cells of babies which then grow to be adults and childeren will exhibit the phenotype
77
how is x chromosome inactivated
coated by xist rna, hypoacetylation of lys in 2 histones. histone methylation.
78
euploidy
complete sets of chromosomes (total x 2 or /1)
79
aneuploidy
loss or gain of one more more chromosomes (i.e. one less in a set)
80
how does monoploidy work
parthenogenesis (development of unfertilized egg into embryo with no fertilization). single set of chromosomes, produce gametes by modified meiosis
81
lethality of monoploidy
ok in male bees, wasps, ants, lethal for other systems because it unmasks recessive lethals. if survives, no meiosis and sterility
82
uses for monoploid plants
visualize recessive traits, introduce mutations
83
how to get monoploid experimentally
haploid pollen treated and plated onto agar, grow embryoids and then treat with hormones
84
polyploidy
common in plants, associated with origin of new species, correlates positively with size and vigor
85
tetraploid plants
alfalfa, coffee, peanuts, large apples, pears, grapes
86
octaploid
big strawberries
87
how are autotriploids fertile
if there are even chromosomes from nondisjunct in meiosis 1
88
how are autotetraploids formed
2n to 4n from spontaneous doubling or drug like colchicine
89
how does tetraploid meiosis happen
1 can sortwith 2 or 3 or 4
90
homeologous
partially homologous chromosomes. like somewhat related plants
91
allopolypoids
hybrid of 2 or more closely related species
92
amphidiploid
douubled diploid (so 4n instead of 2n)
93
you have 2n = 18 parents from 2 different species, what happens when you breed them
gametes of parents are n = 9 and this forms a sterile f1 hybrid n + n = 9 + 9. 2n = 18. This spontenouslly doubles so everyone has a prtner, forming a fertile amphidiploid (2n + 2n = 18 + 18. 4n = 36)
94
nullisomy
2n - 2
95
monosomy
2n - 1
96
trisomy
2n + 1
97
tetrasomy
2n + 2
98
mitotic nondisjunction
results in a mosaic
99
monosomy 21
born with severe multiple abnormalities, dies shortly after birth
100
turner syndrome (XO)
99% of affected fetuses are not born, those that are born have developmental abnormalities
101
down syndrome
21 trisomy, females can be fertile, males infertile, average life expectancy 40-60
102
edward syndrome
trisomy 18
103
patau syndrome
trisomy 13
104
klinefelter syndrome
XXY, some genes expressed at twice the level of XY
105
other types of xy trisomy
XYY: usually fertile, extra y does not pair and not transmitted
XXX: usually fertile, extra x does not pair.
conditions not passed to progeny
106
genomic hybridization: microarrays
detects duplication and deletions of at least 50 kb
107
first trimester screening tests for prenatal testing
nuchal translucency (ultrasound), maternal serum blood tests (placenta hormone levels), noninvaseive prenatal testing (nipt), blood tests
108
diagnostic prenatal testing
chorionic villi sampling (10-13 weeks) using an ultrasound, 1% miscarriage. amniocentesis (16+ weeks) use a needle to get fluid from fetus 0.5%. look for abnormal karyotypes
109
preimplantation embryo diagnosis
screen for mutant alleles before implantation of test tube baby
110
polytene chromosomes
used to study changes in chromosome structure, duplicated a lot without meiosis to form these wiggly things. bandinding can be used to find genes
111
intragenic deletion
small deletion within gene
112
multigenic deletion
many genes deleted, homozygous are usually inviable. heterozygotes may be haploinsufficient
113
pseudodominance
not actully dominant but looks dominant because you deleted an allele which uncovered the mutant gene
114
deletion complementation tests
crossing deletion mutatns to get strains with deletions in differen tplaces. this reveals location of mutant gene
115
duplication
less likely to affect phenotype, most like dosage effect or genetic imbalance, genes may be in new location which modifies expression
116
x ray breakage causing duplication
nontandem duplication
117
unequal crossing over
different number of genes
118
breakpoints between genes
inverted alignment
119
breakpoint within genes
inverted alignment causing disrupted genes
120
breakpoint in 2 genes
fusion of the 2 genes
121
heterozogous inversion
inversion loopsp
122
paracentric inversion
dicentric and acentric fragments. reduced number of viable gametes, deletion products formed
123
pericentri inversion
no dicentric but you still get reduced number of viable gametes
124
translocations
most do not alter phenotype unless breakpoints occur within genes. unless genes are put in some new location that modifies expression'
125
robertsonnian translocation
exchange between acrocentric chromosomes to make a large metacentric and small chromosome that may be lost (basically a big one yoinks the big ar of another, and the small one gets small arm and disappears)
126
robertsonian translocation in madeiran mice
causes loss of a chromosome which causes different numbers of chromosomes
127
translocation homozygote segregation during meiosis
exchange of some genetic material causes the shared part to pair together. there are 3 ways for the 4 chromosomes to separate, and 2 will have deletions or duplications and will die
128
homozygote segregation results
semisterility. < 50% of the time there are viable gametes. pseudolinkage because no independent assortment
129
what is chronic myelogenous leukemia caused by
when c-able and bcr genes are spliced reciprocal translocationally, because they are oncogener and now you dont have normal c-able and bcr mRNA
130
epigenetics
heritable modifications in gene function not due to changes in base sequence of DNA
131
dna methylation at CpG islands, influence in mice
repression of gene expression. the more methylation at the cpg island in mice at iap (retrotransposase insertion), the more grey.shown by mothers diet during pregnancy
132
iap retrotransposase insertion is a what mutation
gain of function that needs to be silenced
133
why is epigenetics needed for normal effect
a cell needs to be able to differentiate
134
drosophila hox gene expression and prc
hox sets up body plan. pre binds to a repressor which binds to a prc. prc will bind to methylation and after several divisions, the methylation will remain where it is. without prc, the methylation will not be retained
135
imprinting epigenetics
methylated with special methylases, demethylated by special demethylases
136
in what phase are parental imprints erased
parents with maternal and paternal imprinted genes are passed onto a zygote which is passed onto BOTH the somatic and germ cells of the child. the child will have erased the old imprints in the germ cells, make new imprints based on maternal or paternal, and now eggs or sperm will have their imprints
137
maternal imprinting for igf2/h19
the igf2 is off, insulator has CTCF dimer on it which is like the donald trump wall, and igf2 is mexico. h19 is america because it has bald eagles and guns, and because ctcf doesn'tb lock it off. the activaotr binding to te enhancer can activate america (h19)
138
paternal imprinting for igf2/ h19
methylation at the insulator AND h19 which means no trump wall (CTCF) and also no activation of america (h19). but without the wall, mexico (igf2) can be activated by the enhancer
139
what does the igf2 do
growth and development of various types of cell tissue in utero
140
does ctcf silencing happen in somatic cells normally
no its a silly thing that only happens in placenta
141
do mutations on the same place for maternal and paternally imprinted chromosomes have the same effects
no, because they may not express the same gene. if its silenced, mutations dont do anything
142
delete igf2 from mother
normal levels of lgf2 because its not expressed anyways
143
delete igf2 from fahter`
no lgf2 and small size
144
prader-willi syndrome
paternal deletion (mutation) from chromosome deletion, obese, small hands and feet, eats uncontrollably, does not mature sexually. since maternal is imprinted, both inactive. if maternal not inactive, it may compensate.
145
angelman syndrome
developmental delay, mental retardation from maternal deletion in chromosome 15. mechanism vice versa for prader-willi
146
benefits for zebrafish
easier to rear for vertebrates, clear embryo, easy microscopy
147
how are living forms related, example with eyes
eyeless (drosophila), pax-6 (mice) and aniridia (humans) are homologous. adding pax-6 to drosophla rescues it from no eye gene.
148
aniridia in humans
partial or complete absense of the iris. sensitivity to light. homozygous is lethal, heterozygote gives you the condition
149
reverse genetics
knockout or mutate certain genes then analyze phenotype
150
forward genetics
need shit ton of mice. mutagenesis following exposure to mutated gene, examine phenotype
151
how is cloning done
donor gives unfertilized eggs, somatic cells' nuclei removed from another animal and put into the egg, embryo grows and put back into surrogate mother to get cloned animal
152
multinucleate syncytium
when there are a shit ton of nuclei and they go out to the cortex. replication of nuclei but no cell division
153
syncytial blastoderm
nuclei go on pilgrimate to edges. pole cells (primordial germ cells) forming
154
how do you screen for mutagenesis to see if a gene is maternal effect or zygotic lethal
feed mutagen, cross with balancer chromosome fly with dominant marker on balancer. balancer inversions prevent recomb. f1 gen will have balancer and a mutation (recessive) and cross this again with the balancer except there is a dominant marker on both chromosomes so you know you don't get the dominant marker instead of the mutation. cross the heterozygous (one wiggly balancer one mutation) and then if homozygous offspring die, it is zygotic lethal, else maternal effect if mothers sterile. check offspring for segmentation
155
gap genes
multisegment that affect many places early. single broad band. include kruppel and knirps.
156
pair rule genes
every other segment. visually, you see 7 segments. even skipped, odd skipped, paired, runt.
157
segment polarity
every segment, 14 of them. gooseberry and patched
158
what do segmentation genes code for
transcription factors for certain proteins
159
how are gap genes activated
maternally provided proteins.for example bicoid bind to cis acting regulatory elements which cause reporter expression
160
bicoid targets
activates hunchback, represses caudal.
161
where are the maternal effect proteins. list from anterior to posterior
bicoid (big range but shit ton on most anterior), giant, hunchback, eve stripe 2, kruppel
162
what activates eve-2
bicoid and giant, inhibited by hunchback ad kruppel
163
how do you find out what activates a specific pair rule or segment polarity gene
by looking at the activators and repressors. then you can put the cis acting regulatory elements onto a plasmid with a reporter gene like gfp that will glow and tell you where shit is. then you put it in am embryo and look at where the glow is :)
164
homeotic mutation
segment characteristic changes (e.g. antenna become legs)
165
how are hox genes normally regulated, where are they present
they are normally in spatially restricted domains, are found throughout the animal kingdom and the order is similar. they limit development of primordial germ cells
166
cancer uncontrolled growth
autocrime stimulation, contact inhibition, cell death, gap junctions.
167
genomic instability
not correcting mismatches
168
angiogenesis
new blood vessels for metastasis
169
multihit model of cancer development
to get a tumor you need several mutations which increases the chance of cells become malignant. (e.g. people get more cancer when they get older)
170
ras
oncongene
171
p53
tumor supressor (it sounds like a gun. guns have suppressors)
172
why do we know cancers are clonal descendants of one cell
get a and b types of tissue, culture them and electrophoresis to compare alleles, compare with tumor
173
evidence from cancer being due to environment
if one sibling or twin gets cancer, other does not mostly. if populations migrate, the chance of getting cancer becomes like the people in new location. cosplayers will get cancer and die, especially me
174
radiation mutagen
x rays and ultraviolet light
175
chemical mutagens
asbestos, cigarette tars
176
virus mutagens
epstein barr (EBV) and human papilloma virus (HPV)
177
protooncogenes
gain of function dominant mutation converts these into oncogenes. inhibit apoptosis and stimulate cell cycle. haploinsufficient
178
tumor-supressor genes
loss of function recessive mutations (DNA repair loss). haplosufficient
179
oncogenes
mutated receptor tyrosine kinase (RTK) genes, ras, bcr, c-abl
180
how do ras proteins promote cell division
when bound to gtp, it creates a map signal cascate and proliferation. it is chill when bound to gdp
181
receptor tyrosine kinases
you have 2, her2 and egf. when they are chilling, they are only activated when binding to signal. if the valine is mutated to glutamine, they will be always dimerized. in the case of EGF, it turns into ErbB oncoprotein which has the extracellular part gone. for the Her2, it turns into the neu oncoprotein
182
how does ras work
inactive binds to gdp, sos stimulates gdp to become gtp, which activates ras. gtp ras will activate downstream serine and threonine kinase. gap turns it off, without gap it is always on
183
how does rb stop tumors
it binds to E2F. phen phosphorylated by cdk4-cyclin d and cdk2-cyclin e, it no longer inhibits ef2. the not inhibited ef2 will start s phase more quickly
184
xeroderma pigmentosum
defect in nucleotide excision remair cause uv induced skin cancers (dimer excision)
185
hereditary nonpolyposis colorectal cancer
defect in mismatch repair. mutations in msh2 or mlh1 are more common, predisposition for colon and ovarian cancer
186
how you you get predisposed for retinoblastoma
by being heterozygous for it because there will be divisions that turn the other into mutant as well and that causes the tumor. it appears autosomal dominant but is actually recessive
