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111 Cards in this Set
- Front
- Back
Where is DNA found in the chloroplast and mitochondria? What shape is it? |
Stroma of chloroplast, matrix of mitochondria, closed and circular |
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What are Chargaff's rules? |
All members of species have same percentage of 4 bases A%=T% and G%=C% |
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Who performed studies using mice and bacteria, showing that transformation of non-pathogenic bacteria occured? |
Griffith
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Who injected mice with DNAse to prove that DNA was responsible for the transformation killing the mice? |
Avery |
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Who determined that bacteriaphage inject DNA into their victim, not protein, using labeled S and P? |
Hershey-Chase |
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Who got the first X-ray structure of DNA |
Rosalind Franklin |
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Who determined the binding patterns of DNA |
Watson-Crick |
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How many bonds to A/T and G/C have? |
2/3 |
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What are the basic characteristics of DNA structure? |
Antiparallel, right-handed double helix, sugar-phosphage backbone on the outside |
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Which type of DNA is left-handed? |
Z |
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What direction is positive supercoiling, and where is it seen to occur? |
In the same direction as the helix (right handed) Compaction of DNA / Barr Bodies |
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What direction is negative supercoiling, and where is it seen? |
Direction opposite to helical winding DNA denaturation, transcriptino and replication |
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What is responsible for supercoiling? |
Gyrase |
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What is Tm? |
Point where 50% of DNA is separated. Higher if there is more G/C |
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What are topoisomerases? Which type cuts 1 / 2 strands? Which type is gyrase? |
relieve overwinding due to supercoiling. Type 1 cuts 1 strand, type 2 cuts 2. Gyrase is type 2. |
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Size of genomes? |
virals: 300 - 2.5mbp Proks: 3E5 to 8mbp plants: as big as 1E11 humans: 3E9 |
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What is the C-Value Paradox? |
The variance in genome size between organisms of similar complexity. |
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What were restriction enzymes originally used for? How do they work? |
Bacterial antivirals. Recognize recognitions sequences, cut them into restriction fragments. |
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What charge is DNA and how does that work for Gel Electrophoresis? How can restriction enzymes be used with this? |
Negatively charged, pulled to positive end of battery. Restriction enzymes used to cut and make restriction map. |
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5 Steps of southern blotting? |
Restriction cutting. Electrophoresis. Blotting. Probing (Radioactive) Autoradiography. |
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What technique is mainly used for sequencing? How does it work? |
Sanger Dideoxy fluroescently labels ddNTPs and watches the order in which they are sequenced. ddNTP prematurely cancels elongation of strand. |
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What percentage of the genome is composed of tandem repeats? Where are they found and what function do they serve? What is the most important tandem repeat? |
10-15% cluster around centromere, serve as attachment of spindle fibers during cell division. telomeres are the most important tandem repeat. (TTAGGG) |
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Which enzyme replaces telomeres? In which type of cells does this occur? |
Telomerase. Germ line cells. |
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What are the various size categories of tandem repeats, and how are they used in forensics? |
Satellite: 1E5 - 1E7 minisatellite: 1E2 - 1E5 Microsatellite: 1-4bp repeats, up to 200 bp site Individual variation allows for genome identification |
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What are three disorders caused by tandem repeats? |
Huntington's Fragile X Myotonic Dystrophy |
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What percentage of the genome is composed of interspersed repeated DNA? |
25-40% |
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How is DNA packaged in Prokaryotes? |
negative supercoiling, wrapped around basic protein cores, in a NUCLEOID. often attached to membrane or wall. |
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What are typical genes found on plasmids, and how long do they take to replicate? |
fertility, antibiotic resistance, toxins 20 minutes |
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How is DNA packaged in euks? Terms for loosely /tightly packed DNA? |
nucleosome beads formed by DNA and basic histone proteins held by ionic bonds. (H2a, 2b, 3, 4) Histone 1 compacts beads into chromatin fibers, which are further looped by nonhistone proteins. Euchromatin / Heterochromatin. |
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How many membranes does the nuclear envelope have? |
2 |
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What is the name for the space between the nuclear membranes? |
perinuclear space |
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What is a nuclear localization sequence? |
amino acid sequence which targets proteins to the nucleus |
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What is the nuclear lamina? |
protein sheath lining the inside of the inner nuclear membrane. |
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What is the role of the nucleolus? |
ribosome factory. |
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What is the nucleolus organizer region (NOR)? |
rRNA gene repeat region |
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How much time does cell replication take for mammals? How much of that time is mitosis? |
18-24 hours 1 hour |
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What are the 3 stages of interphase, and their characteristics? |
G1: checkpoint with possible entry into G0 8-10 hours S: DNA replication 6-8 hours G2: another checkpoint 4-6 hours |
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What cells are normally in G0? |
Neurons hepatic cells immune system cells |
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What is the term for how DNA replicates? Who performed experiments to demonstrate it, and what heavy ion was used? |
Semiconservative Meselson-Stahl N15 |
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How many replication origins do bacteria have? Euks? |
1 many |
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Detail Bacterial DNA replication initiation: What's different for euks? |
initiator protein binds at origin DNA unwinds DNA polymerase accesses interior of helix 5-3 synthesis Euks have multiple proteins, origin recognition complex, and multiple orgins of replication. |
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What is the term for DNA polymerase with it's subunit molecules? |
holoenzyme |
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What enzyme unwinds the DNA for replication? is this energy dependent? |
helicase, yes |
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Which DNA polymerase is used for replication in proks? euks? Where are new NTPs added? |
DNA Pol III / alpha 3' OH |
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What type of proofreading is done by most DNA pols? |
3-5 exonuclease |
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How long are okazaki fragments? |
1-2 thousand ps for proks 1-10 of that for euks |
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How long are RNA primers for DNA replication? Are they needed for each lagging strand fragment? What enzyme makesthem? What replaces them? |
1-10nt's yes. primase DNA Pol I |
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Explain the roles of these players in replication: SSPs topoisomerases ligase |
hold strands apart relieve tension from overwinding Attach sections of DNA |
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Is gyrase ahead or behind of the fork? |
ahead |
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What causes the end gap problem? |
No 3' OH to replace primers |
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What are the three stages of PCR? What species provides the polymerase? |
denaturation Annealing Elongation Thermus Aquaticus |
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How does mismatch repair work? what type of problem does it fix? How does it know which is the parent strand? |
Wrong nucleotide inserted
endonuclease nicks the backbone exonuclease removes the bad boy parent has methylated adenines |
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How does Nucleotide Excision Repair work? What does it fix? Which skin condition is associated with this mechanism? |
thymine dimers and bulky damage single cuts on both sides of distortion by NER endonuclease helicase unwinds DNA DNA Pol fills in gap ligase seals it xeroderma pgmentosum |
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How does Base Pair Excision work? What does it fix? |
Base cleaved off the sugar endonuclease cuts on one side of sugar, removes it Polymerase replaces it |
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What are the 2 techniques for repairing double stranded breaks? |
Nonhomologous end joining: messy Homologous recombination: uses other copy of chromosome for a map |
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Main differences between uracil and thymine? |
Uracil is cheaper. Cytosine deaminates into it, so it would cause problems in DNA code. Thymine has addition CH3 group. |
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What happens in prophase? |
chromosomes condense sister chromatids held at centromeres nucleolus vanishes centrosomes move towards poles |
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What happens in prometaphase: |
nuclear envelope disappears kinetochore forms at centromeres, spindle fibers attach, begin to move |
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How does tubulin subunit subtraction work? Addition? |
subtracted from kinetochore microtubules, shortening them and pulling the chromosomes towards the poles. Addition to polar microtubules pushes the poles apart. |
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Where does ATP-dependent motor action happen in mitosis? |
Kinetochore and centrosome, pulls chromosomes towards centrosomes pushes antiparallel microtubules apart where astral microtubules attach centrosomes to cell cortex, pulls centrosomes to poles |
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How does cytokinesis happen in animals? Plants? |
Cleavage: cleavage furrows form, contractile ring of actin and myosin causes pinching. No cleavage: cell plate forms by mictrotubule array of phragmoplast which forms wall |
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What does the checkpoing in mitosis check for? |
Makes sure all chromosomes are attached to spindle prior to anaphase |
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What molecule rises and falls during the cell cycle, and helps trigger replication and mitosis and that? |
cyclins / Cdk proteins |
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What are homologous chroosomes? |
Pairs of chromosomes (1 from each parent) |
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Term for when both traits are expressed? Where is this seen? |
Codimance AB blood type / Sickle cell |
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Term for when trait is only present in one copy: |
hemizygous |
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Which organisms are always haploid? briefly diploid? alternate generations? |
bacteria fungi mosses |
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When does cross over occur? |
Pachytene stage of prophase 1 |
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At what stage in prophase 1 do duplicated homologous chromosomes begin to par as a tetrad? What is this process called? What is the complex called? |
zygotene synapsis synaptonemal complex |
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What is chiasma? At what stage is it seen? At what point is it the only connection between the chromosomes? |
The visible part of crossover action. diplotene. diakinesis. |
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What are the stages of prophase 1? |
leptotene zygotene pachytene diplotene diakinesis |
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After meiosis 1, are cells haploid or diploid? |
haploid, but with duplicated chromosomes |
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How many total polar bodies are formed? |
3 |
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When can nondisjunction occur? |
anapase 1: homologous chromosomes anaphase 2: sister chromatids |
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What is aneuploidy? Associated diseases? |
having a bad number of chromosomes klinefelter, turner, downs |
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What is a genetic chimera? |
when nondisjunction occurs in mitosis |
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What was the result of Mendel's F1? F2? |
All the same phenotype (heterozygous) 1/4 vs 3/4 phenotypes |
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Mendel's Laws: |
Inheritance is Discrete 2 alleles of gene are distinct independent assortment |
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5 parts of chromosomal theory of inheritance? |
Nuclei have pairs of homologous chrmosomes (one from each parent) chromosomes retain individuality parental chromosomes synapse each member of homologous pair is functionally equivalent parental members segregate independently |
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What is a linkage group? |
genes with loci on same chromosome |
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How is genetic mapping done? |
every 1% of recombination is used as a centimorgan distance unit. |
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How does viral recombination occur? |
coinfection (often in pigs) |
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What type of phage puts its genome into host genome? What are the implications of this? |
Transducing phage. Transfer of host genome to next host is possible. Shigella toxin given to E. coli in this manner |
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How does bacterial conjugation occur? What factor is necessary for this to occur? what are hfr cells? |
F+ donor cell forms F-pilus with F- acceptor, mating bridge is formed. F-factor encoded on F-plasmid. F-plasmid integrated into chromosome, cell is now capable of transferring genomic DNA during conjugation. |
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Difference between transformation and transfection? What is electroporation? |
Transformation i with plasmids, cosmids, artificial chromosomes. transfection is with phage or viral vectors. electric current used to drive DNA into cells. |
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Difference between genomic and cDNA libraries? |
genomic: full genome cDNA: reverse transcriptase used to look at only the genes being expressed. |
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what does agrobacterium tumiaciens do? |
puts Ti plasmid into plants that forms gall and lets it live. Useful for plant genetic modification. |
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What are auxotrophs? |
mutants unable to grow without nutritional supplement |
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What end of tRNA is charged with the amino acid? |
3' |
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Role of: snRNA snoRNA SRP rna siRNA |
forms spliceosome processing of rRNA transcripts in nucleus signal peptide recognition of peptides targeted to RER regulation of gene expression |
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Which DNA strand is read when making the RNA? Which actually has the gene sequence present on the formed RNA? |
Template (antisense) and coding (sense) |
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How many RNA polymerases are there for proks? euks? |
1 3 |
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What subunits comprise the core enzyme of RNA polymerase? |
2 alpha, beta, and beta prime |
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What does the holoenzyme consist of for RNA polymerase in proks? |
core enzyme plus sigma factor |
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what is a transcription unit? |
single stretch of DNA transcribed into single RNA molecule. |
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What is an operon? |
polycistronic string with multiple genes |
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Detail Transcription for proks: |
holoenzyme binds upstream of promoter element (-10 and -35 elements) helicase unwinds synthesis begins (PPi released) (springs forward 7-8bp's at a time) sigma factor comes off (after~9nt's) core enzyme continues synthesizing 5-3 termination signal or rho sequence |
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Detail termination signal based termination and rho terminatino in proks: |
Termination signal encountered, GC-hairpin loop formed followed by string of U's. loop pulls the weak U's off the DNA, and deattachment happens. rho sequence encountered, rho factor (protein) binds to this sequence and ATP unwinds the RNA from the DNA, deattachment occurs |
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What do Euk RNA Pols I-III synthesize? where are they foud |
I: 28, 18, and 5.8S rRNA (nucleolus) II: mRNA and snRNA (nucleoplasm) III: tRNA, 5S rRNA (nucleolus) |
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What are the main 4 promoter elements for Euk transcription? what combinations are seen? |
Initiator region: 1nt upstream, generally A TATA box: 25bp upstream TFIIB (BRE): upstream of TATA DPE: 30bp downstream from startpoint TATA/Inr/BRE DPE/Inr/ |
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What do the TFII's do? |
D: binds to TATA A: binds to DNA B: binds to D F: Binds to PolII and B, bring the Pol in E/H: whatever |
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How does termination occur for RNA Pols I and III in euks? |
I/III: termination signals, no hairpins II: endonuclease cleaves mRNA 10-35nt's downstream from AAUAAA sequence. poly A tail added to tail. |
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What percentage of all RNAs do m, r, and t compose? |
r: 7-80 t: 10-20 m: less than 10 |
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can eukaryotic mRNA sequences code for multiple proteins? proks? |
no yes |
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What S units to prokaryotic rRNAs have? euks? |
50S (23, 5) 30S (16) 60S (28, 5.8, 5) 40S (18) |
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Which rRNA S unit is a ribozyme? |
28S |
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What are tandem arrays for rRNA? How are they processed? Which Pol is responsible for this? |
multipe copies of pre-rRNA genes (except for 5S), separated by spacers. Spacers must be cut out. (snoRNAs) Methyl groups added to 2' OH of ribose RNA Pol I |
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how are tRNA units processed? |
5' leader sequence removed CCA must be at 3' end 15% of bases are chemically modified may need intron removal folded into 4-5 clover shape 70-90nt's |
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How is mRNA processed? |
5'-5' cap added (7-methyl guanosine) some caps may methylate the next 2 bases Poly-A-tail added after transcript is cleaved, for protection and recognition for transport (not H1) Introns removed by spliceosome (snRNP/A 5' site cleaved, makes 2'-5' bond with A inside of intron, 3' site cleaved, and exons are joined. |
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What are the 2 self-splicing mechanisms? where are they found? |
1: no production of lariat (fungi, plants, phage 2: forms lariat (fungus, plant, protist) |
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What is the purpose of Guide RNA? What are some specific changes seen? |
Helps modify transcripts accordingly. C's turned into U's, U's turned into C's, A's to I's. |