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93 Cards in this Set
- Front
- Back
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What are the differences between RNA and DNA synthesis? |
1. ribonucleoside triphosphates are monomers 2. Only one strand of DNA is template for RNA 3. No primer is required 4. RNA is unstable and short lived compared to DNA- Which is good because you can regulate the stability. 5. Occurs in the nucleus (in euks) |
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What are some characteristics of the RNA produced by transcription? |
Transcription creates an mRNA strand. 1. Single stranded 2. Complementary to DNA template strand 3. Identical to DNA nontemplate strand but Thymidines replaces with uracil |
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What are the general features of RNA polymerases? |
- Catalyze the synthesis of an RNA complement to DNA 1. Occurs in 5' to 3' direction 2. Nucleophillic attack by 3' OH on the nucleotidyl phosphorus atom with the elmination of pyrophosphate (releases energy) 3. Unwinds and rewinds DNA in the "transcription bubble" |
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Definition: Transcriptional Unit? |
- segment of DNA transcribed to produce one RNA molecule - One or several genes - Includes 5' and 3' non coding regions and the coding region in the middle |
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Definition: Gene? |
-unit of genetic information that controls the synthesis of one protein or structural RNA molecule |
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Definition: Downstream or Upstream? |
- Refers to 3' and 5' regions of a gene. Downstream is the 3' while upstream is the 5' end |
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Definition: Sense or antisense RNA strands? |
-"Sense" strands encode nucleotides that specify amino acids of gene products -"antisense" strands are complementary to "sense" strands. 1. coding strand= sense strand= non template strand ( identical) 2. noncoding strand= antisense strand= template strand (complementary) |
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Multigenic mRNA vs monogenic mRNA - What do they mean? -proks or euks? |
- Multigenic mRNA occurs in prokaryotes, one gene can code for multiple mRNA sequences -monogenic mRNA occurs in eukaryotes, one gene can only code for one mRNA sequence |
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What are the primary transcripts in the nucleus? - Explain the process of transporting to the cytoplasm. |
1. heterogeneous nuclear RNA (hnRNA) 2. Transcripts are coated with RNA binding protein to protect them from RNases. They are then transported through the pores |
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- Polymerase 1; location? Products? - Polymerase 2; location? Products? - Polymerase 3; location? Products? |
1. Nucleolus, rRNA (nor 5s rRNA) 2. Nucleus, Pre-mRNAs, miRNAs 3. Nucleus , tRNA, 5s rRNA, snRNAs |
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What are sigma factors? |
They dictate what group of genes will be transcribed, used for initiation in transcription. |
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What is a DNA- RNA heteroduplex? |
1 strand of DNA and 1 Strand of RNA partially wound together, occurs briefly during enlongation |
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Peritranscriptional modifications vs post transcriptional modifications; Examples |
Peri= during transcription (5' cap which occurs during enlongation) Post= after transcription (polyadenine tail which occurs right after termination and intron splicing which occurs after termination and the tail) |
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1.What is the function of mRNA? 2.rRNA? 3. tRNA? 4.snRNA? |
1."Messenger RNA" code for proteins 2."ribosomal RNA" form the basic structure of the ribosome and catalyze protein synthesis 3. "transfer RNA" central to protein synthesis as adaptors between mRNA and amino acids 4."Small nuclear RNA" function in a variety of nuclear processes, including the splicing of mRNA |
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1. What is the function of snoRNA? 2. scaRNA? 3. miRNA? 4. siRNA? |
1. "Small nucleolar RNA" used to process chemically modified rRNAs 2. "small cajal RNA" used to modify snoRNA and snRNA 3. "micro RNA" regulate gene expression typically by blocking translation of selective mRNAs 4. "small interfering RNA" turn off gene expression by directive degradation of selective mRNAs and the establishment of compact chromatin structures |
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What is the function of other noncoding RNAs? |
function in diverse cell processes, including telomere synthesis, x-chromosome inactivation, and the transport of proteins into the ER |
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What occurs in the nucleolus? |
The nucleolus is the site of rRNA and ribosome synthesis. - there is a large amount of activity - assembly of telomerase and ribosome |
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How many different codon possibilities are there? - What does this mean? |
4^3= 64 different codon possibilities - This means that since there is a different tRNA for every codon and only 20 amino acids the anticodon of of tRNAs can recognize more than one codon (ie. most amino acids have more than one codon) |
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How is the reading frame determined in translation and why is it important? |
The reading frame is determined by the presence of a start codon (AUG) once that start codon is located the ribosome continues to move to the right by 3 nucleotides and reads in order. This is important because if the reading frame is altered it can affect the amino acids that are added thus messing with the entire protein |
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What are the seven properties of the genetic code? |
1- Nucleotide triplet based (codons) 2- code is degenerate or redundant 3- code is non-overlapping 4- Code is comma free 5- Code is ordered 6- code contains start and stop codons 7- Code is nearly universal |
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What is meant by; "The code is degenerate or redundant" What hypothesis was created to explain this? |
Due to the order of the code many amino acids have very similar codons in which if there is a mutation in the third position it will still code the correct amino acid. So the stringency is less in third position. The wobble hyopthesis was created to explain this. |
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How is the code ordered? |
Since there are multiple codon for many amino acids, the codons for the same amino acid are very similar which is why degeneracy in third position is possible. Also the codons for chemically related amino acids are also similar |
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Describe the transfer RNA molecule and what attaches where? |
tRNA is what brings the amino acid to the ribosome so it can be linked together to form the protein. tRNA is shaped like a clover and on the middle leaf is an anticodon which is complementary to the codon in which it is attaching too, therefore the charged amino acid that is located on the "stem" (5' end) is complementary to the anticodon |
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When does the tRNA link to the codon on the mRNA strand? |
At the A site in the ribosome, it then continues over to the P site where a peptide bond forms between in and the new tRNA which added behind and gets released leaves the amino acid behind in the E site. |
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What is the editing function of tRNA synthetase and how does it work? |
Hydrolytic editing checks for correct amino acids by size. Chain runs through complex and if the amino acid fits into the editing site than it is incorrect and will be cleaved from the tRNA. (Somewhat the same idea with DNA polymerase) |
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Prokaryotes vs Eukaryotes... Where are the ribsosomes located, what are their relative sizes? |
Prokaryotes: located throughout the cell large= 50s small= 30s together =70s Eukaryotes: located in cytoplasm frequently in rough ER large= 60s small=40s together= 80s |
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What are ribosomes made of and how many subunits are there? |
By mass= about 50 % protein and about 50 % rRNA (more than 50 proteins and about 4 rRNA) Composed of 2 subunits, one is smaller than the other. |
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Explain the process of initiation of translations.... Proks vs Euks |
Initiation factors form the ribosome and link to the initiator complex (Euks the 5' cap, proks the shine dalgarno sequence) the ribosome then moves to the right until it finds a start codon and the tRNA links in the A site officially starting elongation |
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Describe elongation in translation |
1- complementary tRNA binds to A- site Charged tRNA bound to EF-Tu interacts with A site, when correct codon/anticodon interaction occurs, EF-Tu binds to factor binding center and the EF-Tu hydrolyzes bound GTP and is released 2-Peptide bond formation in P site= peptidyl transferase activity of 23s rRNA, GTP hydrolysis 3- Translocation of ribosome to next codon and tRNA exits through E site |
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What is translocation and what stimulates it? |
EF-G stimulates ribosome translocation. 1- P site moves to E- site 2. A site tRNA moves to P site 3. mRNA moves by 3 nucleotides to expose next codon 4. EF-G hydrolyzes GTP which facilitates translocation |
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Describe the process of termination in translation |
one the ribosome reaches a stop codon in the A site it signals the ribsosome to dissociate and the mRNA strand to degrade and the protein to be releases. Polypeptide released catalyzed by release factors |
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What happens after the protein is released in translation? |
They undergo folding (usually requires proteins called chaparonins) They can be sorted into different cellular compartments They then undergo degradation which is important in maintaining a fresh population of proteins, also a way to regulate protein levels in cell |
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True/ False: There are no known examples of deleterious ("bad") mutations that are thought to have occurred as a form of "adaption" to an endemic infectious disease. |
False- Sickle cell anemia is an example of a deleterious mutation that also makes those infected with it resistant to malaria. |
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True/ False: Mutations in nature that affect phenotypes are usually deleterious and recessive. |
True |
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True/ False: The best way to differentiate between a back mutation and a suppressor mutation is to perform a genetic cross between two individuals of the same species that both are heterozygous for the original mutation. |
False- The best way to differentiate between a back mutation and a suppressor mutation is to perform a genetic cross between one wild type and one mutant type of the same species. |
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True/ False: Mutations are ALWAYS bad for the organism! |
False- mutations are the basis of evolution good or bad. Example of a good mutation is sickle cell anemia because is offered resistance to malaria |
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True/ False: Xeroderma Pigmentosum (XP) involves defects in genes encoding proteins involved in base excision repair. |
False- XP involves defects in 9 different genes six of which are involved in nucleotide excision repair, which is not the same thing as base excision repair |
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True/ False: Glycosylase and AP endonucleases are NOT part of the same DNA repair pathway. |
False- they are both used in base excision repair |
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What is mendel's wrinkles pea caused by? |
Transposon |
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What best describes point mutation? |
a mutation that alters a single nucleotide |
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What doesn't Nitrous acid do to the DNA? |
convert adenine to guanine |
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What causes a formation of a thymine dimer in DNA? |
Ultra violet light |
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Which DNA repair mechanism represents a "last ditch" effort to repair badly damaged DNA? |
Error-prone repair system (sos) |
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Which DNA repair mechanism contains a enzyme called photolyase? |
Photolyase is important in light dependant repair |
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Which DNA repair mechanism relies, in part, upon the activities of rec A? |
Post replication repair |
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What model is used to describe DNA strand exchange during homologous recombination? |
Holliday model |
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What is a spontaneous mutation and what are their rates in prokaryotes and eukaryotes? |
- Occur without a known cause (inherent errors in replication? Unknown agent in environment?) - Very unlikely but higher rate in euks than proks |
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What are induced mutations and what are their frequency? how many genes can be mutated in an organism |
- occur from a known cause such as exposure to a mutagen. - Frequency depends on the exposure agent (the agent, the dosage etc) up to 1 % of all genes can be mutated in an organism |
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What role do mutations play in evolution? |
- Mutations are the raw material of evolution - leads to genetic variation (change in genotype can lead to change in phenotype and can also respond to the environment) |
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Is too high level of mutation possible? |
yes, it can compromise faithful transfer of genetic info from generation to generation (lethal) - a delicate balance is required |
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Can mutations occur in any cell at any time? Do they always have the same affect? |
Yes they can but no they do not always have the same affect. Example: a mutation in a gene involved in embryonic skeletal development that occurs in a skin cell of an 80 year old This will have no affect on the 80 year old but if it happened in the skeletal cells of an infant it could be tragic |
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What are the effects of mutations in Germ-line cells? Somatic Cells? |
Germ line cells- cells that give rise to gametes so the mutation has an increased probability of being passed down to offspring Somatic cells- all other cells, wont be passed down |
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What is a forward mutation? |
change from Wild-type to mutant phenotype |
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What is a reverse mutation and two examples. |
- Restoration of Wild type phenotype Back mutation- second mutation at the same site as the first to correct or mask first mutation Suppressor mutation- second mutation anywhere in the genome to compensate for effect of first mutation |
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How do you test for a reverse mutation? What are the outcomes? |
Do a back cross: cross a mutant with a true breading wild type= either reverse mutation 1 or 2 Cross again If you have 1 the offspring will be all wild type If you have 2 the offspring will be a mix of wild type and mutant |
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What are the phenotypic effects of mutations? |
Usually deleterious and recessive - Heterozygous tend to have no affect on the phenotype and mutations are not dominate -Most result in an amino acid change that is deleterious to protein function |
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What is a point mutation? Transition? Transversion? Frameshift? |
-mutation that alters a single nucleotide within a gene - replacement of a purine with a purine or pyrimidine with a pyrimidine - Replacement of a purine with a pyrimidine or vice versa - Base pair addition of deletion in gene (alter reading frame |
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Chemical mutagens: Base analogs? |
- Structure is similar to a normal base and is incorporated into DNA during replication - Increases mispairing |
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Chemical mutagens: Nitrous Acid? |
- deaminates amino groups - Results in Transitions |
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Chemical mutagens: Acridine Dyes? |
-Intercalates into DNA -Increases rigidity - induces bends/ kinks - results in additions/ deletions during replication - Nonfunctional proteins |
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Chemical mutagens: Alkylating agents? |
- Transfer alkyl group to base at N or O - Alter bp potential - induce transitions, transversion, frameshift |
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Chemical mutagens: Hydroxylating agents? |
Attaches an OH to amino groups in cytosine which causes it pair with adenine - Results in transversion (g/c to a/t) |
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nonchemical mutagen: UV radiation? |
- Pyrimidines and purines absorb max at 254 nm - UV excites bases causing pyrimidine dimers and pyrimidine hydrates |
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nonchemical mutagen: Ionizing radiation? |
- Xrays, gamma rays, amd cosmic rays - causes increased reactivity of bases - No safe level |
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nonchemical mutagen: transposon? |
-DNA fragments that can move from one site in the genome to another site -insertion of a transposon into an expressed gene will often render gene non-functional EX) mendel wrinkled pea |
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Can DNA ever be read without opening the double helix? |
yes, the outside of the helix can be read by binding proteins without unwinding |
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What model did Jacob and Monod come up with? |
Operon model- Negative control mechanism for inducible or repressible expression |
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What are the two controlling elements of the operon model? What are the components of an operon? |
-1) Repressor- regulator protein that represses transcription 2) operator- site on DNA in which the repressor binds - 1) Set of contiguous structural genes 2) promoter 3) operator 4) multigenic mRNAs |
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What is the structural gene? |
operon genes grouped together to enable coordinated regulation of sets of genes encoding proteins that carry out a specific function |
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What is an example of a negative control inducible operon system? -What is the regulatory gene and some general features? |
The lac operon - lacl is the regulatory gene that codes for the repressor - active as a tetramer (four identical polypeptide chains) - Binds lac operator -lac z, lac y, and lac a - genes to be expressed or not expressed |
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What happens during induction of lac operon? |
inducer is allolactose- it binds to the repressor. - repressor releases from operator and transcription is induced. |
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what prevents expression of the lac operon? What is it called? What is it mediated by? |
-Glucose prevents expression of the lac operon because it is the preferred energy source. - Catabolite repression - Mediated by CAP which binds to cAMP when that is present. (the promoter contains CAP/cAMP binding site) |
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What does the promoter in glucose repressed lac operon contain? |
CAP/cAMP binding site and RNA polymerase binding site |
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What is the cAMP molecule and what is the relationship between it and glucose levels? |
-Effector molecule (cyclic AMP) -Low glucose= high cAMP -High glucose= low cAMP |
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What happens when glucose is low during lac operon? |
CAP binds to cAMP and the complex binds to the promoter allowing trascription |
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What happens when glucose is high during lac operon? |
CAP and cAMP do not form a complex transcription does not get induced |
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What is DNA methylation? |
Changes to the DNA that has nothing to do with the base sequence, not genetic necessarily. |
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What happens during Methylation of cytosine? |
alters recognition by proteins -usually found in base pair doublets forms CpG islands because they are unevenly distributed across the genome. |
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What are CpG islands and where are they found? |
Found near transcription start sites - In humans they are rarely methylated - altered nucleosome, less H1 and acetylated histones - Hypersensitive to DNase1 Methylated CpG associated with repressed transcription |
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What is the mechanism of methylated DNA? What are some important facts? |
The mechanism is not fully understood - two proteins that repress transcription are known to bind to methylated DNA - one of which is MeCP2, changes chromatin structure - suggests that mCpG bind protein complex that represses nearby genes |
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How is methylation involved in imprinting? |
- gene expression is controlled by its parental origin - 20 examples in humans and mice |
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What happens in offspring when methylation is established in the parental germ line? What is this an example of? |
-Somatic cells develop with the same methylation pattern - Germ line methylation is erased and reestablished if oogenesis occurs - Imprinting |
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What is dosage compensation? What are 3 methods to respond to this? |
involved in the sex chromosomes (XX, XY) (X inactivation) Expression on X genes means females have double the expression which leads to hyperactivation. -Inactivation, hyperactivation, hypoactivation |
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Explain the process of X inactivation |
- Occurs in mammalian females - Begins at site called x inactivation center (XIC), spreading in opposite directions towards end of chromosome - XIST gene (w. 17kb RNA) is still expressed on an inactive chromosome. Binds and coats inactive chromosome, nuclear localization |
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Explain the development after the process of X activation |
- Early, Both X chromosomes express XIST - later: XIST transcript from one chromosome stabilize and envelop whole X chromosome --> XIST transcripts from other, disintegrate and expression is repressed by methylation of promoter - Random which X will become inactive |
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What are some examples of inactivation? |
- During interphase, forms darkly staining mass called barr body - during S phase, decondenses and is replicated after all other chromosomes - Have low levels of acetylated histone H4 |
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Explain the process of hyperactivation |
-Drosphila males - complex proteins and RNA bind to specific sites on male X chromosome (only expressed in males) -Binds to 30-40 sites - Likely to be involved in chromatin remodeling because one gene encodes a helicase and another gene is a histone acetyl transferase |
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Explain the process of hypoactivation |
- Caenorhabditis elegans females - exact mechanism is not known - protein binds specifically to both x chromosomes in females but not the x in males - results in repression of expression on both female x chromosomes |
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Explain alternative splicing of mRNA |
-splicesomes in nucleus remove introns - can modify coding sequence by removing exons --> dependent on RNA/ splicesome interaction --> economizes on genetic information --> create numerous related yet different proteins |
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describe mRNA stability. What determines its life time? |
mRNA in cytoplasm can be translated by several ribosomes simultaneously - this continues until mRNA is degraded - Lifetime is determined by 1) length of poly A tail 2) 3' UTR sequence (AUUA promotes rapid degradation) 3) metabolic state of the cell 4) regulatory mechanism |
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What are the two RNA dependent regulations of gene expression? |
1. Directed degradation of mRNA 2. Translational inhibition of specific mRNAs |
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When was Directed degradation of mRNA first observed? |
while performing negative control on antisense experiment. -intro of dsRNA homologous to gene of choice results in a much more efficient silencing than either sense or antisense alone |
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Can amplification of RNAi signal occur? if so how? |
Yes The single stranded siRNA or cleaved mRNA may be the template of RNA-dependent RNA polymerase Which would create more gene specific dsRNAs to be cleaved by dicer and feed into the RNAi pathway |
