MBB 331 - Midterm 3 UPDATED ACTUAL Questions and CORRECT Answers
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MBB 331
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MBB 331
MBB 331 - Midterm 3 UPDATED
ACTUAL Questions and CORRECT
Answers
what is chromatin? - eukaryotic DNA in complex with masses of protein (histones)
what are histones? - proteins that help chromatin fold to be packaged into the nucleus
what is DNA that is wound around histones called? - nucleos...
MBB 331 - Midterm 3 UPDATED
ACTUAL Questions and CORRECT
Answers
what is chromatin? - eukaryotic DNA in complex with masses of protein (histones)
what are histones? - proteins that help chromatin fold to be packaged into the nucleus
what is DNA that is wound around histones called? - nucleosomes
how much DNA does a eukaryotic chromosome contain? - ~2m long in humans
what are the three levels of DNA condensation? - - nucleosome: basic unit
- chromatin: beads on a string, conformation most of the time
- chromosome: most condensed
when would you find DNA compact into chromosomes? - during meiosis or mitosis (dividing
cells)
how many bp of DNA fit into a nucleosome? - 200 bp, including core and linker DNA
t or f:
the bacterial chromosome also contains nucleosomes - false
it is bound by proteins, but does not form nucleosomes
what are considered the building blocks of chromosomes? - nucleosomes
how would you determine nucleosome repeat length experimentally? - - micrococcal
nuclease (not affected by cell age or culturing state)
,- DNA bound by histones cannot be cut
- incomplete digestion results in fragments differing in 200 bp
- length of nucleosome repeat must be 200 bp
what are the 5 histones? - - H1 (linker)
- H2A, H2B, H3, H4 (core)
what histone varies among organisms? - H1
what do the core histones share? - common structural fold, the regions of the histone-fold
motif form alpha helices (cylinders)
what composition of amino acids do histones have? - lysine and arginine because they are
abundantly positively charged
how is a nucleosome assembled? - - initiated by H3(2)-H4(2) tetramer
- binds to dsDNA
- tetramer recruits two copies of H2A-H2B dimer to complete
how are the tails of histones removed? - treated with protease which specifically remove the
amino terminal tails (because they are accessible) that leave the core intact
how do we know that DNA wraps around the histone core? - crystallography
what kind of wrap does the DNA do around the histone core? - left-handed solenoidal
supercoiling around the histone-fold motif
what positions do the histone tails emerge from the core? - - H3 and H2B emerge between the
two DNA helices
- H4 and H2A emerge from either below or above the double helix
what is the histone fold motif? - where the DNA wraps around
,what are the histone tails? - N terminal and C terminal
what part of the DNA do the core histones make contact with? - the minor groove
t or f:
histone tails contribute to DNA binding - false
they don't contribute to DNA binding but mediate inter-nucleosome connections that affect
chromatin structures (compaction level)
what does the structural change of chromatin rely on? - the modification of histone tails
which affect DNA replication, repair, and transcription (epigenetics)
what does the addition of H1 cause? - more compact nucleosomal DNA, the core histones
and H1 protect a larger amount of DNA meaning there is greater compaction
how many binding sites does H1 have? - two DNA binding sites, one that binds to linker
DNA and the other that binds to the DNA wrapping around the core histones
what kind of pattern does H1 create in DNA? - zigzag pattern by bringing the entry and exit
very close together
what is 30 nm fiber/filament? - higher order of organization of nucleosomes thought to exist
in living cells
what are the two models of the 30 nm fiber? - - solenoid model: one-start helix
- zigzag model: two-start helix (not double stranded)
what form are sites of active DNA in (transcription and replication, etc)? - 10 nm fibre
("naked" DNA)
, what could you treat 30 nm fiber with to expand them? - low salt buffer to reveal the loops
what is the majority of DNA packaged into? - large loops of 30 nm fiber that is tethered to the
chromosome scaffold at their base
why is scaffolding needed in DNA? - because there is so much DNA in eukaryotic organisms
that its packaging needs organization, provided by scaffolds
how is bacterial DNA organized? - since it lacks nucleosomes, its compacted into looped
domains attached to one or more points on the inner surface of the plasma membrane
mediated by SMC proteins that organize the circular chromosome into a scaffold like
structure
what controls accessibility to DNA? - nucleosomes control the accessibility of DNA to
transcriptional machinery (RNAP and regulatory proteins)
what are the "open" and "closed" chromatin states associated with? - - "open" active gene
transcription
- "closed" transcription repression
what are the characteristics of nucleosome free zones? - control regions of active genes and
are DNase hypersensitive
what is DNase hypersensitivity? - corresponds to the presence of gene-specific factors
(transcription factors) that exclude nucleosomes from active genes, but not from inactive
genes
what occurs if chromatin is treated with DNase I? - digested DNA is isolated to see the
distance from the known restriction site to determine the hypersensitive site
- inactive gene: no DNase hypersensitivity
- active gene: DNase hypersensitive regions are digested
how can repression caused by H1 be counteracted? - by transcription factors such as Sp1 and
GAL4 which are anti-repressors of histones, they remove nucleosomes that obscure a
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