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Flashcards in Practice Exam 2 2013 Deck (23)

what is the commonly used descriptive term for chromatin strands at 1st level of packing?

DNA with separate unconnected nucleosomes

~150 bp per nucleosome separated by ~50bp linker DNA

"beads on a string"


histones can be extracted from a mitotic chromosome. what ~ fraction of weight of original chromosome does this remove? what is resulting structure

removing histones removes 50% of weight

remaining structure is other proteins (1/3 remaining mass(

loose un-supercoiled DNA still attached to scaffold in largo loops


how are g-bands numbered?

number of chromosome 1st followed by "p" or "q" for the short arm or long arm respectively followed by # of G-band

band #s start at centromere and move out toward telomeres on each arm independently


what does a researcher have to do to investigate an aneuploid child and determine stage of meiosis when nondisjunction occured

karyotype both parents and child and G-band to detect small differences in homologs of affected chromosome

trisomy is typical and 2/3 of the homologs comes from 1 of the parents (in which nondisjunction occured)

if two homologs from the parent are identical then nondisjuction occurred in Meiosis II

if two homologs from that parent include both his/her homologs then it occurred in meiosis I


what different nondisjunctional pathways cause Klinefelter?

nondisjunction in meiosis I or II in mother (creating XX egg)

nondisjunction in meiosis I of father (XY sperm)


where on chromosome of E. coli does process of replication begin? where does it end?

begins at ori sequence

ends on other side of circular chromosome where forks meet


why is primase not required when DNA is copied in a test tube

a short DNA primer is supplied in the test tube


on chromosomal DNA some genes run right-to-left and some left-to-right. does this make a difference in the direction of replication?

no, b/c a gene operates by transcription, not replication

they both go 5' to 3'


when a new aa is added to a growing pp is the pp transferred in the same direction as mRNA moves or opposite direction?

opposite direction

mRNA translocation the codon at P site moves forward to E site

in bond transfer the pp is at P site and moves to A site

in short, it moves from tRNA at P site to tRNA at A site


why doesnt alt. splicing make defective proteins?

exons in coding sequences correspond to separate functional regions of the protein (protein domains)

protein domains are complete functional subunits and reappear in different combinations of different proteins


what factor determines whether proteins get synthesized into ER or cytoplasm?

for ER proteins the first aas on the n-terminus are a signal sequence recognized by a molecule called signal recognition particle

SRP guides signal sequence through a pore into ER so growing pp is inside ER


where is stop codon located in relation to 3' UTR

stop codon is last part of ORF before 5' end of the 3' UTR


if an intron didn't get spliced out what could happen to the protein produced by the mRNA?

intron would be included in the mRNA so when ribosome reads it, the protein would probably be non-functional

"codon" in intron could be stop so the protein could be shorter, intron might be inside a codon, # nucleotides may not be a multiple of 3 so protein might shift to different ORF


what does lac operon produce and under what conditions

produces an mRNA coding for proteins required for metabolism of lactose

conditions are lactose present and glucose levels are low


when does it make sense for an operon to be inducible

when the proteins it codes for are not needed all of the time

makes sense because it avoids using raw materials all the time


overall role of CAP-cAMP system in E. coli

prohibit use of any energy substrate except glucose as long as glucose is available


E. coli can shut down transcription of trp operon but it has an even faster way than that to shut down production of trp.

what is that way, why is it faster, why have both ways?

excess trp directly inhibits 1st enzyme in trp synthesis pathway (faster) than shutting down operon

shutting down operon not as fast b/c pre-existing enzymes still make trp for a while

cell needs enzyme shut-down method b/c if it could only shut down transcription, pre-existing enzymes would continue to make trp until the enzymes degenerated (waste of raw material)

operon shut-down needed b/c if cell could only shut down enzymes, the operon would keep making enzymes wasting raw materials/energy making proteins


histone tails from one nucleosome can attach and hold a nucleosome beside it. what does this tell you about the way in which histone modification affects gene expression

histone tail modification adjusts how tightly or loosely coiled chromatin is, to control accessibility of DNA for transcription

histone tails binding to adjacent histones suggests this is how histones control chromatin compaction

histone modifications directly affect how the tails grab other nucleosomes, governing str. and geometry of how nucleosomes stick together


do only eukaryotes have both cis and trans aspects of gene regulation?

no, they both have cis and trans

prokaryotes have controlling regions of DNA close to promotors (cis), which are binding targets of TFs (trans)


explain how a mutation 5000 nucleotides upstream of a promotor might produce a change in the expression of a gene and therefore a change in phenotype

result of a change in binding affinity for a TF binding site in a CRM


what is the typical structure of the part (domain) of a TF that directly binds to a target site in DNA? what is the typical part of the DNA double helix where the TF binds?

in most TFs the part that recognizes DNA target is an alpha helix

the DNA target sequence is recognized within the major groove of the DNA helix


how does topoisomerase II work?

double-strand break where 2 strands of dsDNA cross

pass intact strand through gap between broken ends

reattach broken ends


what job do sigma factors do in gene regulation

enable specific groups (modules) of operons to be turned on simultaneously in bacteria