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142 Cards in this Set
- Front
- Back
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what are tissue specific enhancers |
some transcripts are only expressed in certain tissues |
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what are the two strategies tha t bring differential gene expression in embryos |
1. maternal derived transcription factors can be localized in different regions of egg 2. cells can communicate with intercellular signals that activate transcription factors asymmetrically |
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what does the egg have within it |
RNA, protein, and nutrients |
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what are maternal gene products |
products produced from mother's genes |
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how do egg cells localize an mRNA to a particular region |
localization signal sequence |
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how does the localization signal sequence move |
the signal sequence binds to a motor protein and that motor protein (myosin) drags the mRNA along an actin filament |
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what is the JAK STAT pathway |
1. ligand binds (cytokinase) 2. causes 2 subunits of receptors to dimerize 3. brings together the cytoplasmic tails of receptors which are bound to JAK 4. phosphorylated tails can bind STAT and STAT is phorphorylated 5. phosphorylated STAT dimerizes and transported to nucleus 6. STAT dimers bind to enhancers and activates transcription |
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what does protein kinase use to phosphorylate a protein |
ATP->ADP |
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what is receptor autophosphorylation |
when cytokinase dimerizes, JAK phosphorylates other JAK molecules |
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what is achondroplasia |
caused by mutated allele for fibroblast growth factor receptor 3. |
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what stage is the fruitfly when it hatches from its eggshell as a worm like |
larva |
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what stage is the fruitfly when it secretes a hard casing |
pupa |
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what was the heidelberg screen |
genetic screen via making mutations to see recessive phenotypes. Revealed 2 distinct non overlapping sets of genes control development along the AP and DV axes respectively |
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how is AP axis established |
asymmetric localization of maternal gene products at the anterior and posterior poles of embryo |
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where is bicoid gene localized |
anterior |
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where is oskar gene localized |
posterior |
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pole cells are found in (oskar/bicoid) |
oskar |
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what do pole cells become |
embryo's germ line |
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where are are the localization sequences in bicoid and oskar found |
3'-UTRs |
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what is the term for the ventral surface bands of fine bristles that help larva crawl |
denticle belts |
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what is the term for the posterior surface structure that supply the embryo with air |
spiracles |
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what is the ligand that surrounds the eggshell of the fruitfly? concentration gradient. |
Spatzle |
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what is the receptor protein that binds spatzle |
toll |
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what does pelle/tube do |
phosporylate cactus to activate it |
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how is cactus activated |
when given the signal, it breaks down resulting in letting go of dorsal so that it can move into the nucleus. |
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where does spatzle normally concentrate |
ventral first |
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what is the mesoderm |
muscle and connective tissue |
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what is neurogenic ectoderm
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CNS |
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order the genes based on activation concentration from highest to lowest |
twist>snail>rhomboid>sog |
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how is it like and unlike DNA sequence recombination |
like: has a specific gene sequence that moves unlike: doesn't have a specific target site |
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what are the two types of transposase |
replicative and non replicative |
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what is the recognition sequence for the transposon |
inverted DNA repeats |
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what happens in insertion |
3'-OH group at end nucleophilically attacks phosphodiester bond on target DNA |
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what happens to the overhangs at site of transposon |
DNA ligase seals the nicks |
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what do RAG-1 and RAG-2 code for |
humane immune system |
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describe the experiment done for the red/white eyes |
2 plasmids were inserted into embryo. plasmid 1 had non autonomous P element; it was replaced with cloned gene X and a marker gene. plasmid 2 didn't have a P element. W+ gene meant red eyes and homozygous W-/W- was for white eyes. COME BACK TO THESE SLIDES |
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what is the Sry gene in charge of |
male and female phenotype |
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what is transgenesis |
the transfer of foreign or modified genes into the genome of a living organism |
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how does random insertion happen in mouse |
injecting many copies of a foreign DNA molecule into the nucleus of a fertilized egg |
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what is a reporter gene |
fusion gene in which an enhancer of one gene is ligated in vitro to a core promoter and the transcription unit of a second gene |
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what are two commonly used reporter proteins |
1. green fluorescent protein (GFP) 2. beta galactosidase- can convert colorless sugar X gal into dark blue |
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what is reverse genetics |
targeted gene knockouts; DNA sequence must be known. |
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what are cleavages in terms of mouse embryogenesis |
divisions of embryo cells |
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what is a blastocyst
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64 cell stage; liquid filled hollow |
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what cells make up blastocyst |
1. inner cell mass or ICM- pluripotent cells known as embryonic stem cells 2. trophectoderm- a monolayer of flat epithelial cells that encapsulate embryo |
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what is an embryo proper |
when blastocyst binds to uterus. and the ICM become the embryo proper to produce the body of mouse pup |
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what does the trophoblast become when the embryo proper develops |
extraembryonic membranes that are part of placenta |
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at the blastocyst stage the ICM cells are (interchangeable/unique) |
interchangable |
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there (is not/ is) an immune system at the blastocyst stage |
is not |
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what is the process of target gene knockout in mice |
1. targeted gene is knocked out by transgene in ES cells in vitro. low success rate so has to be done thousands of times 2. transgenic ES cells are injected into the ICM of host embryo. Embryo is implanted into the uterus of surrogate mother 3. after birth the mouse must be bred through 2 generations to obtain homozygous knock out mouse |
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how is targeted insertion of the knock out transgene accomplished |
homologous recombination |
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in order to have the fosB gene mothers must be (heterozygous/homozygous) (recessive/dominant) |
homozygous dominant |
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what id fosB gene responsible for |
learning and social behaviour; maternal urge |
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what is the inner part of rice |
endosperm; starch |
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inorder to have SCID, patients must have (homozygous/heterozygous) for loss-of-function alleles of the what gene? |
homozygous; adenine deaminase (ADA) |
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what are hematopoetic stem cells |
found in bone that can generate all blood cell types including lymphocytes |
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why are blood cells most ideal for trangenesis |
they can be taken out and put back in |
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why are the complications of insertion of viral vectors |
can result in intergenic insertions or insertional mutagenesis causing loss of function of broken genes |
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what does enzyme RPE65A responsible for and those deficient in this gene are (heterozygous/homozygous) |
blindness; homozygous
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what is the role of trp operon |
1. trptophan is low, the trp is actively expressed 2. trptophan high, the trp operon is inhibited |
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what is trpP |
promoter |
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where does the TrpR repressor bind to |
TrpO |
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where does tryptophan bind to to inactivate trp operon |
tryptophan binds to trpR repressor and represses trp gene. |
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what is attentuation |
addition mechanism that involves premature termination of transcription. |
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what is leader RNA |
structural genes that are not transcribed at the end of trp rna sequence |
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what are the arrangements that leader sequences anneal |
A) 1+2 and 3+4 B) 2+3 |
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what are the organization of the trp operon |
* single promoter-trpP
* 5 structural genes-trpL, trpE, trpC, trpB, trpA * silencing genes-trpO |
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what does the leader peptide consist of |
2 consecutive tryptophan codons midway through it sequence |
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in what organisms is CRISPR found in |
prokaryotes |
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what does CRISPR consist |
conserved and variable spacer sequences |
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what do Cas proteins do |
RNase- cleaves phosphodiester backbone at specific positions within each repeat |
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what are the products of cas cleavage |
crisper RNAs (crRNAs); each has unique spacer sequences between 2 conserved handle sequences. (5' handle and 3'). |
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what is the main purpose of crispr |
targets viruses and bacteriophage DNA to destroy it. Acts as adaptive defense mechanism. Its spacer sequences of CRISPR keep a genetic record of past infections |
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what does the PAZ domain do |
recognize the 3' end of the guide siRNA and positions so it can be cleaved by Argonaute's RNase domain |
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what are microRNAs (miRNAs) |
double stranded regulatory RNAs |
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where can miRNAs be found
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miRNA arises from stem loop in secondary structure of primary transcript. |
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what does Drosha do |
cleaves the pri-mRNA within the nucleus. It cleaves a single phosphodiester bond on either side of the stem loop, releasing the stem loop (aka pre-miRNA) |
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what does Drosha recognize on the step loop |
it recognizes the shape and not the base sequences. The bulges that result from mismatched bases signal to Drosha |
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where does Drosha cut |
separates upper and lower stems
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what is another form of slicing that doesn't involved exons and introns |
presence of 2 or more promoters |
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what does double sex gene encode |
zinc finger transcription factor |
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what is the isoforms of male and female drsophilia and what gene is it |
male:1/3 female:1/2 Dsx |
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how does auto regulation happen in splicing
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the protein produced from the splice site regulates |
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what is immunoglobulin |
antibodies |
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what are non self antigens |
foreign things; not thangs made from the body |
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what part does antigen binding site bind to |
variable regions |
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what is an epitope |
part of antigen that binds to antibody |
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what is the name of the rearrangement of the light chain gene |
VJ rearrangement
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how many segments does the IgG light chain start with |
40 V segments and 5 different j segments |
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how many segments does the IgG heavy chain start with ' |
65 V, 27 D, and 6 C |
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how many segments does the IgG heavy chain start with |
65 V segments
27 D segments 6 J segments |
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what do RAG-1 and RAG-2 do |
they are recombinase proteins |
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when are RAG genes are experssed |
in immature lymphocytes and when gene rearrangement occurs |
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when is the Trp operon silenced |
when tryptophan binds to trpR repressor the repressor becomes active and binds to the trpO gene |
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if trpR gene is deleted does the operon still work |
yes, 3-fold inhibition |
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what is attenuation |
the reduction of trp production due to mutation in gene such as the deletion trpR. Does not alter initiation but causes premature termination. |
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what is attenuation controlled by |
secondary structure of the mRNA |
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what is the intrinsic terminator of transcription in trp mRNA |
hairpin loop |
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how does tryptophan charged aminoacyl tRNA affect the ribosome and trp operon |
it affects how the ribosome translates Trp codons. The tRNA is inversely proportional to the concentration of tryptophan in the cell |
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what happens when 2+3 parts form a hair pin? |
2/3 hairpin is not followed by a string of U's and does not stop transcription |
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what do crRNA do |
they find the complementary DNA sequence and cleave part of the DNA. |
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when the phage infects bacterium what part of its DNA is cut and put into the DNA of the bacterium |
the protospacer that lies adjacent to conserved marker sequence "PAM" |
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if the bacterium has already been infected by a phage that has the same protospacer and PAM, what happens |
crRNA will target phage for degradation by Cas enzymes |
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what is RNA interference |
RNAi; produces a knockdown. Activated by dsRNAs entering cells |
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what does Dicer do |
cleaves the dsRNA more or less randomly into 22 bp fragments; first step of RNAi. Produces siRNAs (small interfering RNAs) |
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what is RISC |
RNA Induced Silencing Complex. Binds to mature ds siRNA, causing it to denature. Guide strand targets RISC to RNAs and passeenger strand is degraded. |
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what is argonaute |
RNase that has a PAZ domain |
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what can the RISC:siRNA complex do |
it can bind to complementary mRNA, prevent translation; degrade RNA; and use the template for producing more siRNA molecules |
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once the pre miRNA is cleaved by Drosha, what happens |
transported to cytoplasm and cleaved off by Dicer |
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how are dicer and drosha similar |
they leave a 3' overhang that is 2 nucleotides in length |
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what are some differences between siRNAs and miRNAs |
miRNAs have sequences that match specific protein coding mRNAs; miRNA can spcifically down regulate the expression of some complementary genes. |
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in some miRNAs (either/left side) is the guide strand |
either |
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what are piRNAs |
piwi-interacting RNAs. Interact with germ cell protein called piwi to silence any transposons that share base pair sequence with the piRNA using methylation |
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why do piRNAs silence transposon
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they prevent transposons from causing heritable mutations. Methylation in DNA can cause mutagenesis; methylation can activate some previously silenced genes but piRNAs got it covered. |
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what is the branch site |
its where 5' splice site binds covalently to the intron. |
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what is an isoform |
different products from a single pre mRNA |
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what parts do the alpha isoform can be spliced |
1,2,3 and 5 |
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what parts do the beta isoform can be spliced |
1,2,4,5 |
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what is a splice repressor |
proteins that direct the spliceosome away from potential splice site |
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what is a splice activator |
proteins that direct the spliceosome to use a potential splice site |
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do the splice sites have consensus sequences? |
if the sequence is more than 60% consensus it can splice
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what happens in fruitfly sex determination |
the ratio of X chromosomes autosomes determines gender. |
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what are autosomes |
non sex chromosomes |
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what are the four key genes that determine sex in drosophila |
1. doublesex 2. sex lethal 3. transformer 4. transformer-2 |
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what does Sxl, tra, and tra-2 code |
sxl- splice repressor protein tra&tra-2- splice activator proteins |
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in females, sxl binds with and what does it do |
own sxl premRNA, tra&tra-2 pre mRNA. Prevents inclusion of male specific exon.
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what do tra/tra2 proteins do |
attract spliceosome to exon 2 causing it to be included in female isoform |
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what does sxl do in male fruitflies |
theres no expression of the protein |
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what are the promoters for sxl |
Pm-maintenance promoter and produces different exon1 pe-early promoter |
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what is the Pe promoter dependent on |
concentrations of activators Sis-a and Sis-b, and repressor Dead pan |
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when is there is 2 copies of sis-a and sis-b while there is 2 copies of dpn, what happens |
Pe is activated; female |
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when is there is 1 copy of sis-a and sis-b while there is 2 copies of dpn, what happens |
Pe silenced; male |
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what is the correlation of sxl and transcripts from Pe and Pm |
Pe- dont require Sxl protein to skip male specific exon Pm- requires functional sxl to skip over specific exon. |
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what is cross hatched |
rearrangement of segments |
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what is NHEJ |
non homologous end joining; anneals DSBs and in doing so adds/removes nucleotides from DSB |
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can the alterations from NHEJ be passed down |
no. Change happens in lymphocytes not in germ line |
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what do hox gene encode |
transcription factors that use homedomain |
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what is the hox gene antennapedia responsible for |
formation of legs |
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how many segments are in each part of a vertebrate animal |
13 segments thorax 6 segments abdomen 4 segments pelvis |
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where is the P element in the fruit fly and where is it silent |
active: egg silent: sperm |
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what part of a blastocyst is the trophectoderm |
the lining |
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what part of a blastocyst is the ICM |
the cells attached to the lining |
