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66 Cards in this Set
- Front
- Back
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What are the three components of Pol 1?
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5'-3' polymerase, 3'-5' exonuclease, and 5'-3' exonuclease.
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What did Cairns in 1969 accomplish?
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He isolated a mutant in Pol 1, with no Pol 1 activity.
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Would you expect this strain to be viable or lethal?
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The expectation is that the DNA polymerase (-) would be lethal.
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Is this a correct assumption?
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No, because there is at least one other DNA polymerase.
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Which of the other two is the key polymerase to allow cell viability?
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DNA Polymerase III is absolutely necessary.
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What is the naming scheme for eukaryotic DNA polymerases?
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alpha:primase(RNA), delta:strand elongation, beta:repair, epsilon:repair, gamma: mitochondria.
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What are the four parts of the flower Arabidopsis flowers?
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The petal, stamen, carpel, and sepal.
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What is the stamen responsible for?
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It is the male part of the plant.
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What is the carpel responsible for?
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It is the female part of the plant.
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How does developmental equivalence relate to the arabidopsis flowers?
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The primordia is initially equivalent, but can adopt any of the 4 fates, but they usually have one set fate.
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What do superman mutants do?
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They increase the number of stamens and carpels.
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Which is affected more, stamens and carpels, and by how much more or less?
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It affects stamens more from 6-12 than carpels from 2-3.
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What does superman encode?
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It encodes a zinc finger domain protein that can act as a transcription factor.
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In an idealized DNA molecule, where is DNA methylated on this molecule?
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The cytosine and adenine are methylated.
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What does this mean?
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It means there is an added methyl group of the adenine and cytosine residues.
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What is the importance of this pertaining to restriction enzymes?
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There are some restriction enzymes that do not cut DNA when methylated at specific bases within the recognition sequence.
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What is DNA methylation known to be important for?
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It is known to be important for X-inactivation, imprinting, methylation of CpG islands, etc.
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What are epi-alleles?
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Epigenetic alleles are not due to changes in DNA sequence but modified in some other way.
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What is complementation or allelism test?
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If m1/m1 has a phenotype, and m2/m2 has the same phenotype, if m1/m2 has the same phenotype, then m1 and m2 are alleles of the same gene.
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What is the assumption ofthe allelism test?
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The assumption is that both mutants are recessive.
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If 2 alleles of the same gene are tightly linked, what does this infer about the frequency of recombination?
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Recombination between 2 alleles in the same gene should be rare.
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What occurs during the complementation test part 2?
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If a wild-type copy of a gene is taken and the mutant is rescued, the defective activity in the mutant is fixed by the wild-type gene product.
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What are mutants?
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They are variants that have a mutation in a specific gene and are stable.
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What are alleles called that make no detectable protein?
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They are considered nulls or amorphs.
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How often does reversion occur for this kind of mutation?
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Very rarely.
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Why did the scientists make a glabrous double mutant to look at reversion?
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They did it to control for cross pollination / contamination.
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What is bisulfite sequencing?
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It is when C is converted to U (T).
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How is this controlled?
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Methyl C is nonreactive and will stay as a C.
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How is bisulfite sequencing utilized?
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Typically, bisulfite and regular sequences will be run side-by-side.
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What is an anti-sense line?
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Expression of an RNA molecule complentary to an mRNA can in some situations, inhibit transcription of that gene and cause a phenotype.
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Is DNA still accessable when in chromatin?
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Yes.
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What role do proteins play with chromatin?
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They play an important role in the condensation of DNA andf the accessability of DNA.
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What do post-translational modifications compose?
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They compose a histone code.
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In which phase, interphase or mitosis is DNA extremely condensed?
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In mitosis DNA is very condensed.
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What is euchromatin?
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It is true chromatin.
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Is euchromatin more or less condensed than heterochromatin?
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It is less condensed.
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Is euchromatin gene poor or gene rich?
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It is gene rich.
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What is euchromatin composed of?
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It is composed of 30 nm fibers and loops.
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Does euchromatin replicate early or late?
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It replicates early.
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What is heterochromatin known as?
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It is known as other or different.
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Is heterochromatin more or less condensed?
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It is more condensed.
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Is heterochromatin gene rich or gene poor?
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It is gene poor.
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What is heterochromatin composed of?
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It is complexed with other proteins.
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Does heterochromatin replicate late or early?
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Late
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What is the compaction profile of euchromatin?
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Short region of DNA double helix gets wrapped up into beads on a string (chromatin). Many of these beads on a string pack together in nucleosomes. These nucleosomes make up a section of chromosome in its extended form. These sections make up a condensed section of chromosome. These condensed sections make up the entire mitotic chromosome.
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What are the two types of proteins that complex with DNA?
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Histones and Non-histone chromosomal proteins.
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How can nucleosomes be isolated?
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They can be digested with nucleases that cut between the nucleosomes in a region called the linker.
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What are the component parts of the nucleosome-octamer?
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2 H2As, H2Bs, H3s, and H4s.
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What does H1 bind?
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H1 binds the linker region.
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How many hydrogen bonds exist between DNA and the nucleosome, and what two things are they mostly between?
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There are 142 hydrogen bonds between DNA and the nucleosome, mostly between phosphodiester bonds and the amino acid backbone of histones.
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What property would you predict of amino acids that contact/stabilize DNA?
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They woulod be rich in positively charged amino acids (R, K)
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What are the N terminal tails subject to?
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They are subject to covalent modification, which is important for transcription.
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What do histones prefer to bind to?
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They prefer to bind to AT rich sequences.
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Can they bind to GC rich sequences?
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Yes, they can.
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What does histone H1 monomers do?
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They link nucleosomes.
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Do other proteins also bind to DNA?
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Yes, they do.
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Under what conditions does it become necessary for nucleosomes to be disrupted and reformed?
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They are disrupted and reformed for replication, transcription, and repair.
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What does the acetylation modification state mean?
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It means gene expression and histone deposition.
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What does unmodified state mean?
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Gene silencing
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What does the methylated state mean?
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It means gene silencing / heterochromatin.
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What does the phosphorylated state mean?
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It means mitosis / meiosis.
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What does the phosphorylated / acetylated state mean?
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Gene expression.
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What are loops associated with areas of?
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They are associated with areas of active transcription in interphase chromosomes.
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In the direction of transcription of a chromatin loop, which is the end closest to the movement of the polymerase called?
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The proximal end.
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In the direction of transcription of a chromatin loop, what is the middle called?
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The middle.
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What is the far end called?
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The distal end.
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