Final Exam Terms (including MI and MII) Flashcards
alpha-amanitin
this is a poison from capped mushrooms that blocks the translocation of bases to the next in RNA Pol; therefore, the pol halts because the bridge cannot move and elongate with the function of the Pol
TATA box
a string of ATATAT sequences that TBP and TAFs can recognize and bind to (though TBP can bind at TATA-less regions as well); strong promoter; recruit site of the RNA holoenzyme; upstream of initiation site
TFIID
First thing that gets recruited on the DNA; contains TBP and TAFs (which are TBP-associated factors); bends the DNA 90 degrees and uses beta sheets to interact with the minor groove of the DNA
TFIIB
Gets recruited along with TFIIA in the next step of the PIC recruitment process; it helps make sure and orients the RNA Pol in the right way
TFIIA
Gets recruited along with TFIIB in the second step of PIC formation; helps stabilizes the TFs-DNA already on there
TFIIH
helps unwind the DNA for RNA transcription; additionally, it acts to phosphorylate the Ser5 on the CTD to allow for the RNA Pol to start moving
RNA Pol II CTD
VERY CRUCIAL aspect; the phosphorylation, methylation, and ubiquitination determines how the RNA Pol acts (i.e., should it wait for the cap to come on before continuing the elongation etc. etc.); it is a 52 conserved sequence region made of heptad YSPTSPS repeats in mammales (26 in yeasts). Hotspot for reversible phosphorylation by kinases and phosphatases
two-hybrid screen
developed in yeasts; attach different genes to two different segments and see if they interact at all
mRNA decay
regulatory control; half-life for bacteria is short (within like minutes) because it is co-transcriptional whereas for eukaryotes it can take several days. Though we should note that not all bacteria have co-transcriptional regulation SO mRNA decay is a great way for regulation
metaphase chromosome
TIGHTLY wounded together; the histones wound and then cohesion and condensin packs them together into an “X”
C-value paradox
an observation that just because you have a lot more DNA, it does not mean you have a lot more genes. The c-value refers to the amount of DNA per haploid chromosome.
30 nm fibers
nucleosomes pack into helical arrays to form 30 nm fibers; 100 fold compaction HOWEVER this structure is observed in vivo only
nucleosomes
a structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones.
cell cycle (from slides)
In G0 and G1, each chromosome contains one ds linear DNA molecule known as the chromatid. After DNA replication and into G2 and M, chromosomes contain two DNA molecules (sister chromatids). Interphase chromatin is less condensed than mitotic chromatin.
histones
nucleosome core that does not have the DNA wrapped around it; just the protein
limited nuclease digestion
releases mono-, di- , and tri- nucleosomes by cutting linker DNA. If you added a really high concentration of nucleases, it would be a smear because it will then break down the di- and tri- nucleosomes
structure of nucleosome core
contains core histones (H2A, H2B, H3, and H4) that are highly conserved among eukaryotes. The core histones associate into heterodimers (H2A-H2B), (H3-H4); or tetramers (H3-H4)2; or octamers (H2A-H2B-H3-H4)2, which are stabilized by hydrophobic interactions. H1 is the linker histone and binds outside the nucleosome core.
dyad axis
pseudo-twofold axis that is common in the nucleosome structure (see L17 slide 15)
What are the nucleotide differences between the major and minor grooves?
AT bp are found more in the minor groove because they are more compressible as compared to GC (this is also known as the 10 bp periodicity in AT and GC bp)
histone tail acetylation
this PTM commonly happen on H3 and H4 tails and this helps separate the DNA so that transcription is a lot easier. Addition of the acetyl group neutralizes this positive charge and hence reduces the binding between histones and DNA, leading to a more open structure which is more accessible to the transcriptional machinery. Histone acetylation therefore leads to transcriptional activation.
histone tail methylation
Methylation and demethylation of histones turns the genes in DNA “off” and “on,” respectively, either by loosening their tails, thereby allowing transcription factors and other proteins to access the DNA, or by encompassing their tails around the DNA, thereby restricting access to the DNA. Methylation activates or represses gene expression depending on which residue is methylated.
centromere
the region of a chromosome to which the microtubules of the spindle attach, via the kinetochore, during cell division; has CENP-A instead of H3 in the histones
phosphatase
dephosphorylates molecules
kinase
phosphorylates molecules
phosphorylation
adding a phosphate group to something - usually via PTM – modification purposes
leading strand
in replication, the strand that is continuously being replicated by the DNA Pol (the 5’ -> 3’)
lagging strand
in replication, the strand that is being synthesized after the leading strand –> this is also the strand that stops and buffers because of the Pol
end replication problem
when you remove the RNA primers, you don’t have a duplex at the end - ssDNA that can be vulnerable to exonucleases -> can be fixed by telomerase
telomerase
an enzyme that fixes the end replication problem using its own template to extend and then reverse transcribe
telomere
a long region of repeats at the end of the chromosome - helps solve the end replication problem
reverse transcriptase
enzyme that converts RNA to cDNA
m7G cap
cap added at the 5’ end of the mRNA and is crucial for translation (because the factors have to recognize it here) and crucial for circularization and protection of the mRNA
