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Biochem formosa
drew
43
Medical
Graduate
02/22/2009

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Term
α-satellites
Definition
172 bp sequence that is repeated about 5 x 105 times (~3% of the genome) in blocks that include the centromeres of each chromosome
Term
Microsatellites
Definition
2-64 base pairs per repeat unit, 3-100s of tandem repeats, don't make up much of the genome. Also called hypervariable regions (HVRs) or variable number of tandem repeat regions (VNTRs). These are used in genomic fingerprinting
Term
What's the most abundant classifiable group of components in the human genome?
Definition
transposable elements or transposons; these make up about 20% of the genome
Term
What are retroposons?
Definition
transposons that move through an RNA intermediate
Term
What are lines? About how many base pairs?
Definition
a type of retroposon; About 500,000 partial copies (of a ~6000 bp intact element)
Term
What are SINEs? How many bp?
Definition
a type of retroposon; SINEs are short (~300 bp), are found in most higher eukaryotes, and do not encode
anything
Term
beads-on-a-string
Definition
The 10 nm fiber. The length of this structure is about 1/6 the length of the DNA it contains.
Term
30 nm fiber
Definition
nucleosomes contact one another to form a higher-order 2-start helix. The length of a 30 nm fiber is about 1/40 the length of the DNA it contains.
Term
euchromatin
Definition
Less compact form of DNA. Usually transcribed.
Term
important steps in prokaryote transcription
Definition
haloenzyme forms a complex with a sigma subunit bound to a promoter, RNA polymerase binds pribnow box and forms stable closed complex, RNA polymerase acts as a helicase and forms the open complex, sigma subunit releases and elongation occurs.
Term
rifampicin
Definition
antibiotic that targets prokaryotic mRNA polymerase
Term
α-amanitin
Definition
Targets Eukaryotic RNA Pol II
Term
Bromodomains
Definition
small (~100 amino acid) motifs found in chromatin proteins that
specifically recognize particular acetylated histone residues
Term
Chromodomains
Definition
small structural motifs that bind to methylated residues
Term
Histone Code
Definition
pattern of modifications is read by proteins with these binding motifs, and they then take the information and alter the expression pattern of the region
Term
Rett's Syndrome
Definition
One of the proteins that binds to methylated DNA in humans is MeCP2, which binds modified DNA and recruits an HDAC complex. Mutations in the MeCP2 gene lead to a type of mental retardation known as Rett's Syndrome
Term
Decitabine
Definition
pyrimidine analog that cannot be methylated. In trial for use in some cancers.
Term
Chromatin Remodelers
Definition
Repositions nucleosomes. Like helicases, this involves hydrolyzing ATP to move along DNA. Unlike helicases, it does not involve separating the DNA strands. Instead, the movement seems to be used to pull DNA to break histone:DNA contacts to move the nucleosomes around
Term
cis
Definition
only affect the expression of the DNA molecules that contain them. Promoter sequences act in cis
Term
trans
Definition
binding proteins themselves act in trans, because they affect any DNA molecule in the cell with their recognition site, not just the DNA molecule that encoded them.
Term
the Mediator
Definition
General transcription factor that recruits Pol II
Term
enhancers and silencers
Definition
In eukaryotes, can be anywhere relative to the promoter and effect the strength of the promoter respecive to the name
Term
operators
Definition
In prokaryotes, sequences called operators modulate the promoter activity; they are usually very near to or overlap the promoter
Term
How does miRNA come from dsRNA
Definition
first digested in the nucleus by an endonuclease called Drosha, then further digested in the cytoplasm by dicer, RISC binds it and blocks translation of mRNA with the same sequence.
Term
All tRNAs must end in?
Definition
5'...CCA-3'
Term
ADARs (adenosine deaminases that act on RNA)
Definition
converts specific adenosines to inosines (which base pair with cytosine instead of with uracil)
Term
ApoB-100 and ApoB-48 are examples of what?
Definition
mRNA processing, cytosine deamination to produce Uracil which introduces a stop codon halfway through the transcript.
Term
RNA splicing
Definition
controlled by spliceosome, 5 ribonucleoprotein (RNP) complexes (called U1, U2, U4, U5, and U6 in
humans). Contain snRNPs, Ribozymes.
Term
Splice sites
Definition
Most introns start with the sequence "GU..." and end "...AG" but many exceptions exist.
Introns contain an adenosine 20-40 nucleotides upstream of the 3' splice site that serves as the branchpoint in the catalytic mechanism.
Term
MutS is involved in what type of repair
Definition
mismatch repair
Term
Migration of a Holliday junction away from the site at which it was formed can lead to a defect that would most likely be repaired by?
Definition
MMR
Term
lariat
Definition
involved in splicing. The 2'OH of a specific adenosine in the intron attacks the 5' splice site, thereby forming the lariat
Term
eIF-2
Definition
Eukaryotic initiation factor. Important in regulating the rate of translation
Term
Shine-Dalgarno sequences
Definition
Prokaryote RBS (ribosome binding sequence.) 6 base sequence found just upstream of the start signal that is complementary to a sequence in the 16S rRNA.
Term
Glucosylation
Definition
acts as a temporary signal indicating an unfolded state
Term
neuraminidase
Definition
viral enzyme that destroys sialic acid; the drugs Relenza
and Tamiflu work by inhibiting neuraminidase so the virus can't escape to infect another cell).
Term
lectins
Definition
polysacharide recognition particles. Can read glycosalation and help navigate cells to a destination
Term
microfilament
Definition
The 2-stranded right-handed polymeric form of actin
Term
centrosome
Definition
microtubule organizing center (MTOC). Contains gamma tubulin which is important for sedding microtubules.
Term
Drugs that destabilize microtubules? How do they work?
Definition
colchicine, colcemid, vinblastine, vincristine. They work by removing the pool of available dimers.
Term
drug that stabilizes MTs
Definition
taxol
Term
Intermediate filaments (3)
Definition
The only ones mentioned were lamin, which composes the nuclear lamina, Cell-cell junctions are associated with vimentin, and Keratin.
Term
multivesicular bodies (MVBs)
Definition
AKA endosomes, central intermediates in sorting of receptor-mediated endocytosis.
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