Glossary of MCB 411 Exam 3 Note Set 2

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

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