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cell bio Q2 > Ch. 4 pt 1 and Ch. 4 pt 2 > Flashcards

Ch. 4 pt 1 and Ch. 4 pt 2 Flashcards

ch. 4 pt 1: 22-32; Ch. 4 pt 2: 1-9 (83 cards)

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1
Q

only about 20% of the genome is….

A

packaged in that portion of the euchromatin associated with the actively expressed genes

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2
Q

20% open, active chromatin can be broken down into…

A

8%- highly accessible promoters, enhancers, active genes

12%- weakly transcribed genes

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3
Q

inactive, closed chromatin is __% euchromatin and __% heterochromatin

A

40 and 40

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4
Q

the 40% of inactive, closed euchromatin is…

A

quiescent, unmarked, linker histone bound

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5
Q

the 40% of inactive, closed heterochromatin is broken into

A

20%- facultative heterochromatin, regulated

20%- constitutive heterochromatin, permanent

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6
Q

facultative heterochromatin, regulated: includes?

A

developmentally repressed genes

marked by H3K27me3 or H3K9me

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7
Q

constitutive heterochromatin, permanent: includes

A

centromeres, telomeres, satellites, other repeats

marked by H3K9me3

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8
Q

chromatin modifiers

A

chemically alter histone proteins in the nucleosome by adding chemical groups to amino acid side chains or by removing them

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9
Q

chromatin modifiers primarily occur at…

A

N-terminal histone tails

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10
Q

chromatin modifiers: modifications include…

A

acetylation
methylation
phosphorylation
ubiquitination
others

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11
Q

histone modifications impact…. and….

A

impact chromatin structure and play a role in gene expression

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12
Q

two main mechanisms by which histone modifications exert their effects

A

directly influencing chromatin structure

building effector molecules to regulate gene expression and other cellular activities

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13
Q

modifications recruit…

A

proteins to alter chromatin structure and regulate gene activity

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14
Q

acetylation _____ chromatin

A

opens

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15
Q

nomenclature:

H3K27me3

A

H3: histone 3
K27: lysine; 27th amino acid
me3: 3 methyl groups

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16
Q

histone modification : H4K4me3

associated with chromatin type:

gene expression:

abundance:

A

histone modification: methylation

associated with chromatin type: highly accessible, open chromatin

gene expression: ON

abundance: 1%

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17
Q

histone modification : H3K9ac

associated with chromatin type:

gene expression:

abundance:

A

histone modification : acetylation

associated with chromatin type: highly accessible, open chromatin

gene expression: ON

abundance: 1%

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18
Q

histone modification : H3K9me3

associated with chromatin type:

gene expression:

abundance:

A

histone modification : methylation

associated with chromatin type: heterochromatin (constitutive or facultative)

gene expression: OFF

abundance: 25%

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19
Q

histone modification : H3K27me3

associated with chromatin type:

gene expression:

abundance:

A

histone modification : methylation

associated with chromatin type: facultative heterochromatin

gene expression: OFF

abundance: 13%

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20
Q

the histone code is a well established hypothesis describing the idea thatspecific patterns of post translational modifications to histones act like a __________ recognized and used by non hisotne porteins to regulate specific ___ functions

A

molecular “code”

specific chromatin functions

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21
Q

the histone code should be considered to be more like a …

A

language

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22
Q

writer reader and eraser proteins

A

writer: chemically modifies the histone

reader: effects the execution of the appropriate biological function

eraser: removes the histone modification

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23
Q

all of the covalent additions to histones are_______, being constantly removed and added at rates that depend on both their _______ locations and specific ______ of the cell.

A

dynamic; chromosomal; states

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24
Q

acetylation writers and erasers

A

writer: histone acetyltransferase (HAT)

eraser: histone deacetylase (HDAC)

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25
methylation writers and erasers
writer: histone methyltransferase (HMT) eraser: histone demethylase (HDMT)
26
methylation may promote activation or repression depending on...
location
27
initially, sequence specific DNA binding proteins (e.g transcription factors) may...
bind DNA and recruit the histone modifying enzymes.
28
transcription regulator (transcription factor)
general name for any protein that binds to a specific DNA sequence to influence the transcription of a gene
29
a generalized sequence of events for activating transcription: 1. _____________________ binds DNA 2. ______ (writer) binds to TF and ________ the histones in the vicinity (nucleoside associate loosens) 3. chromatin remodeling complex ___ the nucleosome, allowing access to the DNA 4. addition ____- bind 5. _____________ binds and transcription begins
1. transcription factor 2. HAT (writer); acetylates 3. slides the nucleosome, allowing access to the DNA 4. TFs 5. RNA polymerase
30
reader-writer after a writer enzyme modifies one or a few nucleosomes...
the writer collaborates with a reader in the same protein complex to spread the modification from nucleosome to nucleosome
31
reader-eraser
a reader eraser complex can reverse the chromatin change
32
barrier DNA sequences mark the boundaries of.... barrier DNA-protein complexes block the spread of...
-chromatin domains - reader-writer complexes
33
two major classes of heterochromatin in mammalian cells
facultative heterochromatin -trimethylation of H3K27 -highly regulated constitutive heterochromatin -trimethylation of H3K9 -permanent
34
function of constitutive heterochromatin
-form the centromere -silence a variety of selfish DNA elements -tightly repress genes that are active early in embryonic development
35
centromeric chromatin
-location of cetromere -constitutive heterochromatin -persists throughout interphase -contains a centromere-specific variant H3 histone: CENP-A -CENP-A plus additional proteins form the kinetochore
36
human centromeres
-over several million nucleotide pairs -do not contain centromere-specific DNA sequence -largely consist of short repeated DNA sequences -there is plasticity of centromere formation
37
faithfully inherited...
once a special region of chromatin forms, this assembly is thereafter faithfully inherited
38
epigenetic inheritance
inheritance of phenotypic changes in a cell or organism that do not result from changes in the nucleotide sequence of DNA
39
epigenetic inheritance can be due to...
positive feedback loops of transcription regulators or to heritable modifications in chromatin such as DNA methylation of histone modification
40
chromosomes occupy...
discrete territories in the nucleus
41
chromosomes are or are not extensively entangled with one another
are not
42
how are heterochromatin and euchromatin distributed differently?
heterochromatin is often closely associated with the nuclear envelope euchromatin extends into the nucleoplasm bay from the nuclear envelope
43
heterochromatin: _____ nearest to periphery _____ interior to ^
H3K9me3 H3k27me3
44
dynamic structure of interphase chromosomes
loops of chromatin expand to occupy an increased volume when a gene within them is expressed
45
the interior fo the nucleus is very ____, with functionally different regions to speed different biochemical processes
heterogeneous
46
topologically associating domains (TADs)
fundamental units of 3D nuclear organization
47
interphase chromosomes are organized as...
long linear series of folded looped domains of chromatin (TADs)
48
roughly ____ loops in the human genome between _____ - ______ nucleotide pairs of DNA, though loops of a million nucleotide pairs also exist
10,000 50,000-200,000
49
DNA sequences within a TAD...
physically interact with each other more frequently than with sequences outside of that domain
50
TADS partition the genome into
distinct regulatory territories
51
TADS: likely function in regulation of gene expression by...
limiting enhancer-promoter interactions to sequences with a TAD
52
TADs: loop positions can fluctuate, allowing for...
a highly dynamic chromatin structure during interphase
53
disruption of TAD boundaries may result in...
a wide range of diseases
54
TAD: the loop extrusion model involves the...
cohesion complex to generate loops and CTCF protein to establish the boundaries of the loops
55
SMC proteins are a family of .... that...
family of large ATPases that participate in many aspects of higher order chromosome organization and dynamics
56
SMC stands for
structural maintenance of chromosomes
57
SMC proteins form...
distinct heterodimers that make the core components of multi protein complexes such as cohesion and condensin
58
cohesin: ____ and ____
SMC1 and SMC3
59
condensin: ______ and ________
SMC2 and SMC4
60
what is a SMC protein complex?
a large ring shaped protein complex that uses ATP hydrolysis energy to make the looped domains that organize chromosomes
61
SMC protein complexes include
the eukaryotic cohesin and condensin proteins
62
SMC protein complexes have important roles in....
bacteria, archaea, and eukaryotes
63
the SMC protein is a large protein of ___ to_____ amino acids that folds on itself to form antiparallel coiled coil with a globular head. two of these molecules then pair to produce a ring structure with a ____ at one end an an ___ binding domain at the other end. additional subs are then added to for either __ or ____.
1,000 to 1,5000 flexible hinge ATP cohesin or condensin
64
SMC protein complexes bind and encircle the..
DNA double helix
65
the SMC heterodimers forms a ring that is large enough for...
DNA that is packed in chromatin to readily pass through
66
the SMC ATPase domains allow the ring to...
motor rapidly along DNA
67
the cohesin complex is a protein complex that mediates
DNA looping sister chromatid cohesion homologous recombination other cellular processes
68
cohesin complexes have different subunit compositions for...
different functions
69
text definition of cohesin complex
complex of proteins that uses ATP hydrolysis energy to organize interphase chromosomes into a series of looped domains
70
during mitosis, cohesins also...
hold sister chromatids together along their length before their separation
71
mechanism of TAD formation: loop extrusion model 1. the cohesin complex binds ___ to form a _________. 2. using the energy of _________, cohesin extrudes chromatin on both sides of the ring to ____ the loop 3. cohesin stops when it encounters a chromatin bound ________ protein on each side.
1. chromatin; small DNA loop 2. ATP hydrolysis; enlarge 3. CTCF
72
TAD boundaries are brought together with....
CTCF complexes forming the base of a chromatin loop
73
mitotic chromosomes are _______
highly condensed
74
chromosome folding in M phase: 1. chromatin loops created by cohesin are... 2. ________ begins to form very large chromatin loops organized radially by a .... 3. as _______ loops grow larger, ______ forms a second set of loops within the larger loops. this generates a loops within loops organization 4. along with tighter winding of chromatin loops around the ________, a very compact chromatin is created
1. quickly lost 2. Condensin II; central chromosome axis 3. condesin II, condesin I 4. mitotic chromosome axis
75
genome comparison reveal functional DNA sequences by their....
conservation throughout evolution
76
homologous genes
genes that are similar in both their nucleotide sequence and function because of a common ancestry
77
homologous genes can often be recognized across vast....
phylogenetic differences
78
in general, the sequences of individual genes are much more tightly conserved than is overall ___ structure
genome
79
DNA sequences that are closely similar between different species are through to more likely ....
have a functional conserved DNA regions
80
conserved DNA regions
closely similar pieces of DNA sequence
81
______% of the human genome consists of multi species conserved sequences
4.5%
82
about 1% of multi species conserved species.... the remaining....
code for proteins the remaining : -protein binding site for gene regulation -transcribed into important non coding RNAs
83
an additional 5% of our genome shows a ........, implying that these sequences are also important
reduced variation in the human population

cell bio Q2 (6 decks)

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