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hmb fuck this shit > 2nd half > Flashcards

2nd half Flashcards

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

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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

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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.

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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)

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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.

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6
Q

adeno-associated virus (AAV) applications

A

cystic fibrosis, sickle cell disease, thalassemias, canavan disease (cindy stole talia’s candy)

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7
Q

adenovirus (AV) characteristics

A

large virus, carries large genes, transient expression (not long), evokes immune response, infects dividing and nondividing cells

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8
Q

adenovirus (AV) applications

A

cystic fibrosis, hereditary emphysema, (also used for otc deficiency

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9
Q

herpes characteristics and applications

A

long term expression, infects neuroglia, used for brain tumors.

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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

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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)

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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)

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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

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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

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15
Q

What is SCID X-linked mutations due to

A

deficiency in IL2 receptor gamma

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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

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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

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18
Q

Why does moving LMO increase expression

A

you probably moved it next to an enhancer

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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

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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

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21
Q

how did briard dogs help us know about LCA

A

four nucleotide deletion (AAGA) makes a premature stop codon

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22
Q

What vector was used for RPE65 gene therapy, how was it

A

rAAV2, adult subjects remained healthy

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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

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24
Q

incomplete dominance

A

red and white get pink

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25
Q

codominance

A

black and white get spots

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26
Q

additive inheritance

A

independently segregating loci that adds up, a special type of incomplete dominance

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27
Q

two hypothesis of quantitative traits

A

segregation of alleles at many loci, loci have small, equal, additive effects. quantitative trait can be explained by few genes with large additive effects

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28
Q

quantitative traits are also called

A

polygenic/multifactorial

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29
Q

how is familial hypercholesteraemia an example of incomplete dominance

A

heterozygous phenotype distinct from either homozygous phenotype to get an intermediate

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30
Q

what is qtl (quantitative trait locus)

A

a trait that is affected continuously by the environment and multiple genes. can be masked by environment or the genes

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31
Q

why are complex traits shaped like a normal curve

A

because they are the sum of various phenotypes which form small hills

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32
Q

Vp =

A

Vg + Ve

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33
Q

Vg =

A

Va + Vd + VI

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34
Q

what does broad sense variation document

A

how much phenotypic variation is attributable to genotypic variation

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35
Q

narrow sens variation

A

family specific predictability of phenotype based on parental phenotype. additive effects are the only transmissible effects

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36
Q

what doesnt h^2 tell you

A

whats happening in other families, what the genes are

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37
Q

How to identify a QTL

A

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

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38
Q

lod formula

A

probability of linkage given the recomb rates/probaility of no linkage

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39
Q

how to determine recomb rates for lod

A

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

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40
Q

whats the lod demominator

A

if 11 items. (0.8)^11

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41
Q

what are RILs

A

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

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42
Q

what do you do when you find quantitative trait loci

A

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

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43
Q

what are indel mutations

A

insertion deletion

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44
Q

subsitution mutation

A

base replaced by one of other 3 bases

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45
Q

reciprocal translocation

A

2 nonhomologous chromosomes change places

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46
Q

transition subsitution

A

a to g (purine to purine) or c to t (pyrimidine to pyrimidine)

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47
Q

transversion

A

purine to pyrimidine or vice versa

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48
Q

backgroundrate of mutation

A

2-12 * 10^-6 mutations per gene per gamete

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49
Q

depurination

A

guanine gone (cannot be adenine)

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50
Q

deamination

A

cytosine changed to uracil

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51
Q

x ray mutation

A

deletion

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52
Q

uv light mutation

A

thymine dimer

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53
Q

oxidation

A

guanine to go, which mispairs with A

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54
Q

what do indel mutations cause

A

loops in dna for the loop that has extra with respect to the other

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55
Q

how to know strength of selection for a mutation

A

compare nonsynonymous with synonymous. neutral genes have similar rates

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56
Q

what two types of mutation change length of protein

A

frameshift, nonsense

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57
Q

intragenic supressor mutations

A

a mutation that compensates for another (check)

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58
Q

how can mutations be outside the coding sequence

A

disrupts splice donor and acceptor site

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59
Q

null (amorphic mutation)

A

mutant has the same amount of activity as if its deleted

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60
Q

hypomorphic (leaky) mutation

A

mutant is less severe than straight up deleting the allele

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61
Q

what makes a loss of function mutation haploinsufficient or sufficient?

A

threshold for wt trait

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62
Q

hypermorphic mutation

A

too much prtein

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63
Q

neomorphic mutation

A

protein with new function, or normal protein made at wrong time and place

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64
Q

what does unequal crossing over in human vision do

A

natural variation in r/g vision

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65
Q

alkaptonuria

A

phenylalanine eventually makes homogentistic acid (HA) needs an oxidase to turn it into smth else. without it, HA accumulates and you have black pee

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66
Q

how do biosynth pathways work

A

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

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67
Q

how do you get a partially yellow and purple corn

A

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

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68
Q

how do you get spotted corn

A

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

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69
Q

what is flanked by short repeats

A

transposed DNA

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70
Q

how much of the drosophila and human genome do TEs take up

A

12.5 and 34 respectfully %

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71
Q

after a p element is excised for transposons, how is the gap repaired

A

using a homologous chromosome. transposon will remain in original position if homologous chromosome also has it

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72
Q

What is a line

A

autonomous retrotranposon 1-5kb

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73
Q

What is a sine

A

nonautonomous retrotransposon 100-300kb

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74
Q

why dont TEs kill all of us

A

usually in introns. sometimes dont work because no repeats at the ends. heterochromatin prevent it.

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75
Q

what kinds of mutations could happen with TEs

A

unequal crossing over leading to deletions and duplications, or seeing 2 tes as one big te and yoinking that whole thing

76
Q

how are transposable elements used in the lab

A

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
Q

how is x chromosome inactivated

A

coated by xist rna, hypoacetylation of lys in 2 histones. histone methylation.

78
Q

euploidy

A

complete sets of chromosomes (total x 2 or /1)

79
Q

aneuploidy

A

loss or gain of one more more chromosomes (i.e. one less in a set)

80
Q

how does monoploidy work

A

parthenogenesis (development of unfertilized egg into embryo with no fertilization). single set of chromosomes, produce gametes by modified meiosis

81
Q

lethality of monoploidy

A

ok in male bees, wasps, ants, lethal for other systems because it unmasks recessive lethals. if survives, no meiosis and sterility

82
Q

uses for monoploid plants

A

visualize recessive traits, introduce mutations

83
Q

how to get monoploid experimentally

A

haploid pollen treated and plated onto agar, grow embryoids and then treat with hormones

84
Q

polyploidy

A

common in plants, associated with origin of new species, correlates positively with size and vigor

85
Q

tetraploid plants

A

alfalfa, coffee, peanuts, large apples, pears, grapes

86
Q

octaploid

A

big strawberries

87
Q

how are autotriploids fertile

A

if there are even chromosomes from nondisjunct in meiosis 1

88
Q

how are autotetraploids formed

A

2n to 4n from spontaneous doubling or drug like colchicine

89
Q

how does tetraploid meiosis happen

A

1 can sortwith 2 or 3 or 4

90
Q

homeologous

A

partially homologous chromosomes. like somewhat related plants

91
Q

allopolypoids

A

hybrid of 2 or more closely related species

92
Q

amphidiploid

A

douubled diploid (so 4n instead of 2n)

93
Q

you have 2n = 18 parents from 2 different species, what happens when you breed them

A

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
Q

nullisomy

A

2n - 2

95
Q

monosomy

A

2n - 1

96
Q

trisomy

A

2n + 1

97
Q

tetrasomy

A

2n + 2

98
Q

mitotic nondisjunction

A

results in a mosaic

99
Q

monosomy 21

A

born with severe multiple abnormalities, dies shortly after birth

100
Q

turner syndrome (XO)

A

99% of affected fetuses are not born, those that are born have developmental abnormalities

101
Q

down syndrome

A

21 trisomy, females can be fertile, males infertile, average life expectancy 40-60

102
Q

edward syndrome

A

trisomy 18

103
Q

patau syndrome

A

trisomy 13

104
Q

klinefelter syndrome

A

XXY, some genes expressed at twice the level of XY

105
Q

other types of xy trisomy

A

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
Q

genomic hybridization: microarrays

A

detects duplication and deletions of at least 50 kb

107
Q

first trimester screening tests for prenatal testing

A

nuchal translucency (ultrasound), maternal serum blood tests (placenta hormone levels), noninvaseive prenatal testing (nipt), blood tests

108
Q

diagnostic prenatal testing

A

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
Q

preimplantation embryo diagnosis

A

screen for mutant alleles before implantation of test tube baby

110
Q

polytene chromosomes

A

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
Q

intragenic deletion

A

small deletion within gene

112
Q

multigenic deletion

A

many genes deleted, homozygous are usually inviable. heterozygotes may be haploinsufficient

113
Q

pseudodominance

A

not actully dominant but looks dominant because you deleted an allele which uncovered the mutant gene

114
Q

deletion complementation tests

A

crossing deletion mutatns to get strains with deletions in differen tplaces. this reveals location of mutant gene

115
Q

duplication

A

less likely to affect phenotype, most like dosage effect or genetic imbalance, genes may be in new location which modifies expression

116
Q

x ray breakage causing duplication

A

nontandem duplication

117
Q

unequal crossing over

A

different number of genes

118
Q

breakpoints between genes

A

inverted alignment

119
Q

breakpoint within genes

A

inverted alignment causing disrupted genes

120
Q

breakpoint in 2 genes

A

fusion of the 2 genes

121
Q

heterozogous inversion

A

inversion loopsp

122
Q

paracentric inversion

A

dicentric and acentric fragments. reduced number of viable gametes, deletion products formed

123
Q

pericentri inversion

A

no dicentric but you still get reduced number of viable gametes

124
Q

translocations

A

most do not alter phenotype unless breakpoints occur within genes. unless genes are put in some new location that modifies expression’

125
Q

robertsonnian translocation

A

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
Q

robertsonian translocation in madeiran mice

A

causes loss of a chromosome which causes different numbers of chromosomes

127
Q

translocation homozygote segregation during meiosis

A

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
Q

homozygote segregation results

A

semisterility. < 50% of the time there are viable gametes. pseudolinkage because no independent assortment

129
Q

what is chronic myelogenous leukemia caused by

A

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
Q

epigenetics

A

heritable modifications in gene function not due to changes in base sequence of DNA

131
Q

dna methylation at CpG islands, influence in mice

A

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
Q

iap retrotransposase insertion is a what mutation

A

gain of function that needs to be silenced

133
Q

why is epigenetics needed for normal effect

A

a cell needs to be able to differentiate

134
Q

drosophila hox gene expression and prc

A

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
Q

imprinting epigenetics

A

methylated with special methylases, demethylated by special demethylases

136
Q

in what phase are parental imprints erased

A

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
Q

maternal imprinting for igf2/h19

A

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
Q

paternal imprinting for igf2/ h19

A

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
Q

what does the igf2 do

A

growth and development of various types of cell tissue in utero

140
Q

does ctcf silencing happen in somatic cells normally

A

no its a silly thing that only happens in placenta

141
Q

do mutations on the same place for maternal and paternally imprinted chromosomes have the same effects

A

no, because they may not express the same gene. if its silenced, mutations dont do anything

142
Q

delete igf2 from mother

A

normal levels of lgf2 because its not expressed anyways

143
Q

delete igf2 from fahter`

A

no lgf2 and small size

144
Q

prader-willi syndrome

A

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
Q

angelman syndrome

A

developmental delay, mental retardation from maternal deletion in chromosome 15. mechanism vice versa for prader-willi

146
Q

benefits for zebrafish

A

easier to rear for vertebrates, clear embryo, easy microscopy

147
Q

how are living forms related, example with eyes

A

eyeless (drosophila), pax-6 (mice) and aniridia (humans) are homologous. adding pax-6 to drosophla rescues it from no eye gene.

148
Q

aniridia in humans

A

partial or complete absense of the iris. sensitivity to light. homozygous is lethal, heterozygote gives you the condition

149
Q

reverse genetics

A

knockout or mutate certain genes then analyze phenotype

150
Q

forward genetics

A

need shit ton of mice. mutagenesis following exposure to mutated gene, examine phenotype

151
Q

how is cloning done

A

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
Q

multinucleate syncytium

A

when there are a shit ton of nuclei and they go out to the cortex. replication of nuclei but no cell division

153
Q

syncytial blastoderm

A

nuclei go on pilgrimate to edges. pole cells (primordial germ cells) forming

154
Q

how do you screen for mutagenesis to see if a gene is maternal effect or zygotic lethal

A

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
Q

gap genes

A

multisegment that affect many places early. single broad band. include kruppel and knirps.

156
Q

pair rule genes

A

every other segment. visually, you see 7 segments. even skipped, odd skipped, paired, runt.

157
Q

segment polarity

A

every segment, 14 of them. gooseberry and patched

158
Q

what do segmentation genes code for

A

transcription factors for certain proteins

159
Q

how are gap genes activated

A

maternally provided proteins.for example bicoid bind to cis acting regulatory elements which cause reporter expression

160
Q

bicoid targets

A

activates hunchback, represses caudal.

161
Q

where are the maternal effect proteins. list from anterior to posterior

A

bicoid (big range but shit ton on most anterior), giant, hunchback, eve stripe 2, kruppel

162
Q

what activates eve-2

A

bicoid and giant, inhibited by hunchback ad kruppel

163
Q

how do you find out what activates a specific pair rule or segment polarity gene

A

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
Q

homeotic mutation

A

segment characteristic changes (e.g. antenna become legs)

165
Q

how are hox genes normally regulated, where are they present

A

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
Q

cancer uncontrolled growth

A

autocrime stimulation, contact inhibition, cell death, gap junctions.

167
Q

genomic instability

A

not correcting mismatches

168
Q

angiogenesis

A

new blood vessels for metastasis

169
Q

multihit model of cancer development

A

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
Q

ras

A

oncongene

171
Q

p53

A

tumor supressor (it sounds like a gun. guns have suppressors)

172
Q

why do we know cancers are clonal descendants of one cell

A

get a and b types of tissue, culture them and electrophoresis to compare alleles, compare with tumor

173
Q

evidence from cancer being due to environment

A

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
Q

radiation mutagen

A

x rays and ultraviolet light

175
Q

chemical mutagens

A

asbestos, cigarette tars

176
Q

virus mutagens

A

epstein barr (EBV) and human papilloma virus (HPV)

177
Q

protooncogenes

A

gain of function dominant mutation converts these into oncogenes. inhibit apoptosis and stimulate cell cycle. haploinsufficient

178
Q

tumor-supressor genes

A

loss of function recessive mutations (DNA repair loss). haplosufficient

179
Q

oncogenes

A

mutated receptor tyrosine kinase (RTK) genes, ras, bcr, c-abl

180
Q

how do ras proteins promote cell division

A

when bound to gtp, it creates a map signal cascate and proliferation. it is chill when bound to gdp

181
Q

receptor tyrosine kinases

A

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
Q

how does ras work

A

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
Q

how does rb stop tumors

A

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
Q

xeroderma pigmentosum

A

defect in nucleotide excision remair cause uv induced skin cancers (dimer excision)

185
Q

hereditary nonpolyposis colorectal cancer

A

defect in mismatch repair. mutations in msh2 or mlh1 are more common, predisposition for colon and ovarian cancer

186
Q

how you you get predisposed for retinoblastoma

A

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

hmb fuck this shit (1 decks)

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