Chapter 8

Question 0

A given ___ of __ with its associated ___ is called chromatin.
• Histones are small, basic ___ associated with DNA. Nonhistone proteins are not as abundant, but can regulate ____, __, ___,___.
• ___ are DNA associated with histones. ___ cells have no histones or nucleosomes.

Answer 0

A given region of DNA with its associated protein is called chromatin.
• Histones and non histone proteins. Histones are small, basic proteins associated with DNA. Nonhistone proteins are not as abundant, but can regulate DNA replication, repair, recombination and transcription.
• Nucleosome: DNA associated with histones. Prokaryotic cells have no histones or nucleosomes.

Question 1

Each DNA and its associated protein is called a ___.
A. Packaging DNA into ___ makes the DNA readily fit inside the cell
B. Protects DNA from ___
C. Only packed DNA can be transmitted efficiently to_____
D. The chromosome confers an overall organization to each molecule of DNA, which can regulate the ___ of DNA

Answer 1

Chromosome: each DNA and its associated protein is called a chromosome.
A. Packaging DNA into chromosomes makes the DNA readily fit inside the cell
B. It protects DNA from damage
C. Only packed DNA can be transmitted efficiently to both daughter cells when a cell divides
D. The chromosome confers an overall organization to each molecule of DNA, which can regulate the accessibility of DNA

Question 2

Prokaryotic cells typically have only one copy of their chromosome (s) that is packaged into a structure called ___, which is not ___ from the rest of the cells.

Answer 2

Prokaryotic cells typically have only one copy of their Chromosome (s) that is packaged into a structure called nucleoid, which is not separated from the rest of the cells.

Question 3

Eukaryotic chromosomes are located in the ___-____ nucleus. Haploid (one copy) and diploid
(two copies) cells are distinguished by the ___present in the nucleus.

Answer 3

Eukaryotic chromosomes are located in the membrane-bound nucleus. Haploid (one copy) and diploid
(two copies) cells are distinguished by the number of copies of each chromosome present in the nucleus.

Question 4

The ___, rather than ___, is more closely related to organism complexity. This becomes more clearly when we examine the relative gene density of different genomes.
(___ ____ is more accurate in predicting organism complexity, Humans have ___ (coding) gene density.

Answer 4

The number of genes, rather than genome size, is more closely related to organism complexity. This becomes more clearly when we examine the relative gene density of different genomes.
(Gene density is more accurate in predicting organism complexity, Humans have low (coding) gene density).

Question 5

More complex Organisms have decreased ____. (I.e. E. Coli has high and humans have low)

Answer 5

Comparison of chromosomal gene density for different organisms. More complex Organisms have decreased gene density.

Question 6

Processed pseudogenes arise from integration of _______

Answer 6

Processed pseudogenes arise from integration of reverse-transcribed messenger RNAs

Question 7

Pseudogenes normally lack intron. Why are pseudogenes not expressed?

Answer 7

D

Question 8

____: the sites at which the DNA replication machinery assembles and replication is initiated.

In general ^^^^ are found in ____ regions. They are typically found some 30-40 kb apart throughout the length of each eukaryotic chromosome.

Answer 8

Origin of replication: the sites at which the DNA replication machinery assembles and replication is initiated. In general origins of replication are found in non-coding regions. They are typically found some 30-40 kb apart throughout the length of each eukaryotic chromosome.

Question 9

Centromeres = a specialized structure on the chromosome, appearing during cell division as the ______region where the two chromatids are held together and form an ___ shape. Centromeres are required for correct ___ of the chromosomes after DNA replication. Centromeres direct the ____.

The kinetochore assembles at each ____ DNA, and before chromosome segregation, the kinetochore binds to protein filaments called ____ that eventually pull the sister chromosomes away from each other, and into the two daughter cells.

Answer 9

Centromeres: a specialized structure on the chromosome, appearing during cell division as the constricted central region where the two chromatids are held together and form an X shape. Centromeres are required for correct segregation of the chromosomes after DNA replication. Centromeres direct the formation of an elaborate protein complex called kinetochore.

The kinetochore assembles at each centromere DNA, and before chromosome segregation, the kinetochore binds to protein filaments called microtubules that eventually pull the sister chromosomes away from each other, and into the two daughter cells.

Question 10

___ are located at two ends of a linear chromosomes. ___ proteins distinguish the nature ends of the chromosome from sites of chromosome breakage and other DNA breaks in the cell. Second, telomeres act as specialized _____ that allow the cells to replicate the ends of the linear chromosome. Telomeres facilitate __

Answer 10

Telomeres: are located at two ends of a linear chromosomes.
Telomeric proteins distinguish the nature ends of the chromosome from sites of chromosome breakage and other DNA breaks in the cell.
Second, telomeres act as specialized origins of replication that allow the cells to replicate the ends of the linear chromosome. Telomeres facilitate end replication

Question 11

More than one centromere per chromosome or less than one centromere per chromosome leads to chromosome loss or breakage. If there is exactly one centromere for each chromosome, ___. If there is more than one centromere, ____.
If there is less than one centromere, ____.

Answer 11

If there is exactly one centromere per chromosome, the chromosomes will separate evenly into two daughter cells.
If there is more than one centromere, there will be breakage of the chromosomes because of the multiple centromeres.
If there is less than one centromere, there will be random segregation of chromosomes.

Question 12

Centromere ___ and ___ vary dramatically among different species.

In S phase, sister-chromatid cohesion is established by ring-shaped ___, which are hypothesized to encircle ___ of recently replicated DNA.

Answer 12

Size and composition

In S phase, sister-chromatid cohesion is established by ring-shaped cohesin molecules, which are hypothesized to encircle two copies of recently replicated DNA.

Question 13

A. The two ___ of each linked sister-chromatid pair attach to opposite poles of the mitotic spindle;
B. Once all kinetochores are bound to opposite poles, sister chromatid cohesion is eliminated by ____ (____);
C. After cohesion is eliminated, the sister chromatids are segregated to opposite poles of the mitotic spindle.

Answer 13

The two kinetochore of each linked sister-chromatid pair attach to opposite poles of the mitotic spindle;
B. Once all kinetochores are bound to opposite poles, sister chromatid cohesion is eliminated by destroying the cohesin ring (proteolysis);
C. After cohesion is eliminated, the sister chromatids are segregated to opposite poles of the mitotic Spindle.

Question 14

Chromosomes are maximally condensed in ___ phase and decondensed throughout _____.
DNA replication requires the nearly complete disassembly and reassembly of the ____ associated with each chromosome.
Sister chromatid cohesion is established immediately after ___.
So chromosome is a constantly changing structure that is more like an organelle than a simple string of DNA.

Answer 14

Chromosomes are maximally condensed in M phase and decondensed throughout the rest of cell cycle.
DNA replication requires the nearly complete disassembly and reassembly of the proteins associated with each chromosome.
Sister chromatid cohesion is established immediately after replication.
So chromosome is a constantly changing structure that is more like an organelle than a simple string of DNA.

Question 15

SMC (structural maintenance of chromsome) proteins form defined pairs through the lengthy _____. Together with ____ proteins, they form multiprotein complexes that act to link two DNA helics together.
Cohesin is a SMC-protein-containing complex that is required to link two daughter DNA complexs together after DNA replication. Cohesin structure is a large ring composed of two ___ and two ___.
Condensin: a SMC-containing complex required for chromosome ____. It is also a ring-shaped complex which can link different ____, therefore reducing the overall ___ of the chromosome.

Answer 15

SMC (structural maintenance of chromsome) proteins form defined pairs through the lengthy coiled-coil domains. Together with non-SMC proteins, they form multiprotein complexes that act to link two DNA helics together.
Cohesin is a SMC-protein-containing complex that is required to link two daughter DNA complexs together after DNA Replication. Cohesin structure is a large ring composed of two SMC and two non-SMC proteins.
Condensin: a SMC-containing complex required for chromosome Condensation. It is also a ring-shaped complex which can link different regions of the same chromosome together, therefore reducing the overall linear length of the chromosome.

Question 16

____ and ____ are mediated by SMC proteins

Answer 16

Sister-chromatid cohesion and chromosome condensation are mediated by SMC proteins

Question 17

Interphase: chromosome are in a ____
state. Interphase is composed of _____ .
Prophase: chromosome are ___ and detangled in preparation for segregation, and ___ ___ breaks down
Metaphase: Each sister-chromatid pairs attaches to opposite poles of the ____. Bivalent attachment! (monovalent attachment will lead to ______). Main constituents are the centromere/kinetochore/microtubule).

Answer 17

Interphase: chromosome are in a decondensed
state. (G1, S, G2, DNA replication)

Prophase: chromosome are condensed and detangled in preparation for segregation, and nuclear membrane breaks down

Metaphase: Each sister-chromatid pairs attaches to opposite poles of the mitotic spindle. Bivalent attachment (monovalent attachment will lead to both copies of chromosome moving into one daughter cell) (centromere/kinetochore/microtubules

Question 18

Anaphase: loss of sister-chromatid ___, resulting the separation of sister chromatids.

Telophase: loss of chromosome ____, and reformation of nuclear membrane.

Cytokinesis: ____ surrounding the two nuclei constricts and eventually completely separates into two daughter cells.

Answer 18

Anaphase: loss of sister-chromatid cohesion, resulting the separation of sister chromatids.

Telophase: loss of chromosome condensation, and reformation of nuclear membrane.

Cytokinesis: cellular membrane surrounding the two nuclei constricts and eventually completely separates into two daughter cells.

Question 19

*meiosis: Interphase: G1, S and an ___ G2 phase. DNA replication, and then ___ between ____(one from each parent). Homologous chromosome forms a structure called ____.

Metaphase I: the two kinetochores of each sister- chromatid pair attach to one pole of the ___ spindle. (monovalent attachment! : ______.)
Anaphase I: separation of ___ ____.
Meiosis II: is similar to mitosis. No ____ though. Separation of sister chromatids.

Answer 19

Interphase: G1, S and a elongated G2 phase. DNA replication, and then recombination between homologous non-sister chromosomes (one from each parent). Homologous chromosome forms a structure called chiasma.
Metaphase I: the two kinetochores of each sister- chromatid pair attach to one pole of the meiotic spindle. (monovalent attachment: both kinetochores of each sister chromatid pair are attached to the same pole of the microtubule spindle, this reaction is called monovalent attachment, which is in contrast to the bivalent attachment in mitosis.)
Anaphase I: separation of recombined homologs.
Meiosis II: is similar to mitosis. No DNA replication though. Separation of sister chromatids.

Question 20

After meiosis I& II, the ___ sets of chromosomes are packaged into nuclei and separated into ___ cells to create ___ germ cells.

Answer 20

The 4 sets of chromosomes are packaged into nuclei and separated into fours cells to create 4 germ cells.

Question 21

______: sequence-nonspecific nuclease. The ability of this enzyme to cleave DNA is primarily governed by ____.

Answer 21

Micrococcal nuclease (Mnase): sequence-nonspecific nuclease. The ability of this enzyme to cleave DNA is primarily governed by the accessibility of the DNA.

Question 22

HISTONES: Abundant proteins whose mass in nuclei nearly equals that of DNA. Corresponds to 1 histone octamer per 200 bp of DNA
• Pronounced ___ charge at neutral pH
• Most are well-conserved from one species to another
• Not ___genes, (___ many times)
– Some copies are identical
– Others are quite different
– ___ has only had 2 variants ever reported

Answer 22

Abundant proteins whose mass in nuclei nearly equals that of DNA. Corresponds to 1 histone octamer per 200 bp of DNA
• Pronounced positive charge at neutral pH
• Most are well-conserved from one species to another
• Not single copy genes, repeated many times
– Some copies are identical
– Others are quite different
– H4 has only had 2 variants ever reported

Question 23

The protein core of the nucleosome is a disc-shaped structure that assembles in an ordered fashion only in the presence of DNA. Without DNA, the core histones can form ____

Answer 23

The protein core of the nucleosome is a disc-shaped structure that assembles in an ordered fashion only in the presence of DNA. Without DNA, the core histones can form intermediate assemblies in solution.

Question 24

Assembly of a nucleosome
1. Formation of ___;
2. The tetramer binds to double
strand DNA;
3. The H3•H4 tetramer bound DNA recruits ____ to complete the assembly of nucleosome

Answer 24

Assembly of a nucleosome
1. Formation of H3•H4 tetramer;
2. The tetramer binds to double
strand DNA;
3. The H3•H4 tetramer bound DNA recruits two copies of H2A•H2B dimer to complete the assembly of nucleosome

Question 25

______ of the core histones are accessible to proteases.
Trypsin: specifically cleaves protein after positively charged ____.
The exposed amino-terminal tails are not required for the association of DNA with the histone octamer, because _____.
These amino-terminal tails are the sites of extensive ___ that alter the function of ___.

Answer 25

Amino-terminal tails of the core histones are accessible to proteases
Trypsin: specifically cleaves protein after positively charged amino acids.
The exposed amino-terminal tails are not required for the association of DNA with the histone octamer, because DNA is still tightly associated with the nucleosome after protease treatment.
These amino-terminal tails are the sites of extensive posttranslational modifications that alter the function of individual nucleosomes.

Question 26

The nucleosome has an approximate twofold axis of symmetry
You can think of the face of the octamer disc as a clock with the middle point of the 147bp of DNA located at the ___ o’clock position, this places the ends of DNA just short of 11 and 1 o’clock.
Rotation around the axis 180° reviews a nearly identical view of the nucleosome

Answer 26

The nucleosome has an approximate twofold axis of symmetry
You can think of the face of the octamer disc as a clock with the middle point of the 147bp of DNA located at the 12 o’clock position, this places the ends of DNA just short of 11 and 1 o’clock.
Rotation around the axis 180° reviews a nearly identical view of the nucleosome

Question 27

Many ______ contacts mediate the interaction between the core histones and DNA.
The minor grooves face the histone octamer.
About 40 hydrogen bond between the histones and the DNA.
The majority of these hydrogen bonds are between the __ and the ___ atoms in the phosphodiester backbone near the minor groove of the DNA.
The positive charge of the histones mask the negative charge of the phosphate in DNA, which facilitates ____.

Answer 27

Many DNA sequence- independent contacts mediate the interaction between the core histones and DNA
The minor grooves face the histone octamer.
About 40 hydrogen bond between the histones and the DNA.
The majority of these hydrogen bonds are between the proteins and the oxygen atoms in the phosphodiester backbone near the minor groove of the DNA.
The positive charge of the histones mask the negative charge of the phosphate in DNA, which facilitates DNA bending.

Question 28

The histone amino- terminal tails stabilize _____.
(A)The four H3 and H2B tails emerge between the two helices.
In contrast, the H4 and H2A tails emerge either above or below both DNA helices
(B)The position of the tails relative to the entry and exit of the DNA. (H3, H2B tails equal distance from each other. Same as H4 and H2A).
You can think of ___ as grooves of the screw, directing DNA to wrap around the histone octamer disc in a ___ handed manner.

Answer 28

The histone amino- terminal tails stabilize DNA wrapping
(A)The four H3 and H2B tails emerge between the two helices.
In contrast, the H4 and H2A tails emerge either above or below both DNA helices
(B)The position of the tails relative to the entry and exit of the DNA. (H3, H2B tails equal distance from each other. Same as H4 and H2A).
You can think of histone tails as grooves of the screw, directing DNA to wrap around the histone octamer disc in a left handed manner.

Question 29

Nucleosome stores _____ in eukaryotic cells.
Assembly of nucleosome on covalently closed circular DNA (cccDNA) requires the presence of ____ to accommodate the changes in linking nubmer of the DNA bound to histones.
(a)In the absence of topsoisomerase, the assembly of nucleosomes is limited by the _____ not associated with nucleosomes.
(b)Addition of topoisomerase without additional nucleosome assembly illustrates how topoisomerase reduces the ____ to relax the DNA not incorporated into nucleosomes.
(c)Additional nucleosome assembly in the presence of topoisomerase.
(d)Simutaneous removal of ___ and inactivation of ___ (by adding strong detergent) reveals the reduced inking number associated with nucleosomal DNA.

Answer 29

Nucleosome stores negative superhelicity in eukaryotic cells.
Assembly of nucleosome on covalently closed circular DNA (cccDNA) requires the presence od toposiomerase to accommodate the changes in linking nubmer of the DNA bound to histones.
(a)In the absence of topsoisomerase, the assembly of nucleosomes is limited by the accumulation of positive superhelicity in the DNA not associated with nucleosomes.
(b)Addition of topoisomerase without additional nucleosome assembly illustrates how topoisomerase reduces the linking number to relax the DNA not incorporated into nucleosomes.
(c)Additional nucleosome assembly in the presence of topoisomerase.
(d)Simutaneous removal of histone and inactivation of topoisomerase (by adding strong detergent) reveals the reduced inking number associated with nucleosomal DNA.

Question 30

Nucleosome assembly assay that measures the associated _____ in linking number
cccDNA, Topoisomerase Add strong detergent at different time point (SDS, sodium dodecyl sulfate: inactivates the ___ and at the same time removing the ___ from DNA)
Gel electrophoresis
On average the topoisomerase will have decreased the linking number by ~1.2 for each ____ assembled on the cccDNA

Answer 30

Nucleosome assembly assay that measures the associated decrease in linking number
cccDNA,
Topoisomerase
Add strong detergent at different time point (SDS, sodium dodecyl sulfate: inactivate the topoisomerase and at the same time removing the histone from DNA)
Gel electrophoresis
On average the topoisomerase will have decreased the linking number by ~1.2 for each nucleosome assembled on the cccDNA

Question 31

Heterochromatin: densely stained with a variety of dyes and has more condensed appearance. Limited ____.
• Euchromatin: stained poorly with dyes and has a relatively __ structure. Higher level of _____.
• ___ shows little gene expression, but this doesn’t mean that it is not important. Keeping a gene turned off is as important as turning it on.
• Heterochromatic regions have nucleosomes assembled into higher-order ___ that result in a barrier to ____.

Answer 31

Heterochromatin: densely stained with a variety of dyes and has more condensed appearance. Limited gene expression
• Euchromatin: stained poorly with dyes and has a relative open structure. Higher level of gene expression
• Heterochromatin shows little gene expression, but this doesn’t mean that it is not important. Keeping a gene turned off is as important as turning it on.
• Heterochromatic regions have nucleosomes assembled into higher-order structures that result in a barrier to gene expression.

Question 32

Histone H1 binds two DNA helices
Histone H1 binds to the ___ at one end;
It also binds to the ____ (middle of the associated 147bp) of the nucleosome bound DNA.
Addition of histone H1 protects an additional 20bp of the DNA from micrococcal nuclease digestion.
Histone H1 binding increases the __ of the DNA wrapped tightly around the histone octamer.
H1 binding produces more defined angle of DNA entry and exit from the nucleosome.

Answer 32

Histone H1 binds two
DNA helices
Histone H1 binds to the link DNA at one end;
It also binds to the central DNA helix (middle of the associated 147bp) of the nucleosome bound DNA.
Addition of histone H1 protects an additional 20bp of the DNA from micrococcal nuclease digestion.
Histone H1 binding increases the length of the DNA wrapped tightly around the histone octamer.
H1 binding produces more defined angle of DNA entry and exit from the nucleosome.

Question 33

Two models for the 30-nm chromatin fiber
(A) The solenoid model:bsix nucleosomes form a ____. The linker DNA doesn’t pass through central axis of the superhelix, and the sides and the entry and exit points of the nucleosomes are readily inaccessible.
(B) The zigzag model: the 30nm fiber is a compacted form of the zigzag nucleosome arrays (4 nucleosome for one superhelix). Explain
This condensation results in another six- to seven-fold condensation of the nucleosome itself.

Answer 33

Two models for the 30-
nm chromatin fiber
(A) Thesolenoidmodel:six nucleosomes form a superhelix. The linkder DNA doesn’t pass through central axis of the superhelix, and the sides and the entry and exit points of the nucleosomes are readily inaccessible.
(B) The zigzag model: the 30nm fiber is a compacted form of the zigzag nucleosome arrays (4 nucleosome for one superhelix). The linker DNA frequently pass through the central axis of the fiber, and the sides and even the entry and exit points are more accessible. Longer linker DNA favors this conformation.
This condensation results in another six- to seven-fold condensation of the nucleosome itself

Question 34

The histone amino-terminal tails are required for the formation of ____.
Core histones lacking their ____ are incapable of forming 30-nm fibers.
Speculative model for stabilization of the 30-nm fiber by histone amino –terminal tails.
Shown here is that the amino- terminal tails of ___, ___and ___ interact with adjacent nucleosome cores.

Answer 34

The histone amino-terminal tails are required for the formation of the 30-nm fiber
Core histones lacking their amino- terminal tails are incapable of forming 30-nm fibers.
Speculative model for stabilization of the 30-nm fiber by histone amino –terminal tails.
Shown here is that the amino- terminal tails of H2A, H3 and H4 interact with adjacent nucleosome cores.

Question 35

____ account for most of chromatin in a typical interphase nucleus.
Further folding is required in structures such as the mitotic chromosomes. Model favored for such higher order folding is a series of ___.
The electron-dense regions are nuclear scaffold that acts to ____.
Two classes of proteins that contribute to the nuclear scaffold have been identified: __I (that can hold the DNA at the base of the loops) and ___ (condensins).

Answer 35

30-nm fibers account for most of chromatin in a typical interphase nucleus
Further folding is required in structures such as the mitotic chromosomes
Model favored for such higher order folding is a series of radial loops
The electron-dense regions are nuclear scaffold that acts to organize the large amounts of DNA found in the eukaryotic chromosome.
Two classes of proteins that contribute to the nuclear scaffold have been identified: Topoisomerase II (that can hold the DNA at the base of the loops) and SMC proteins (condensins)

Question 36

H2A. X is a variant of H2A. When chromosome DNA is broken, H2A.X (located adjacent to the break) is ___ not present in H2A. H2A.X phosphorylation is specifically recognized by DNA repair enzyme.
• CENP-A: H3 variant, is associated with nucleosomes that include centrometric DNA (replace H3 in the region). The extended tail of CENP-A is the ___for another protein component of the kinetochore called CENP-C, which ____.
• Loss of CENP-A interferes with the ____ with the centromeric DNA.

Answer 36

H2A. X is a variant of H2A. When chromosome DNA is broen, H2A.X located adjacent to the break is phosphorylated at a serine residue not present in H2A. H2A.X phosphorylation is specifically recognized by DNA repair enzyme.
• CENP-A: H3 variant, is associated with nucleosomes that include centrometric DNA (replace H3 in the region). The extended tail of CENP-A is the binding site for another protein component of the kinetochore called CENP-C, which mediates attachment of chromosome to the mitotic spindle.
• Loss of CENP-A interferes with the association of kinetochore components with the centromeric DNA.

Question 38

Nucleosome-remodeling complexes (NRCs) facilitate changes in ___ or ____ using energy from ATP

Answer 38

Nucleosome-remodeling complexes (NRCs) facilitate changes in nucleosome location or interaction with DNA using energy from ATP

Question 39

All NRCs can catalyze ___.
A subset of NRCs can catalyze more extreme change in which a histone octamer is ejected into solution or ”transferred” from one DNA helix to another.
Some of the enzymes can facilitate the exchange of __with _____

Answer 39

All NRCs can catalyze the sliding of DNA
along the surface of the histone octamers.
A subset of NRCs can catalyze more extreme change in which a histone octamer is ejected into solution or ”transferred” form one DNA helix to another.
Some of the enzymes can facilitate the exchange of H2A/H2B dimer with variants of the dimer.

Question 40

In additional to the intrinsic dynamics shown by the nucleosome, the stability of histone octamer-DNA interaction is influenced by large protein complexes called nucleosome- remodeling complex. The nucleosome- remodeling complexes ______

Answer 40

In additional to the intrinsic dynamics shown by the nucleosome, the stability of histone octamer-DNA interaction is influenced by large protein complexes called nucleosome- remodeling complex. The nucleosome- remodeling complexes bind DNA tightly and position the translocase subunit adjacent to the nucleosomal DNA.

Question 41

By holding the translocase in place relative to the histone octamer, the net results of ____is to move the DNA relative to the surface of the histone octamer.

Answer 41

By holding the translocase in place relative to the histone octamer, the net results of ATP hydrolysis by the nucleosome- remodeling complex is to move the DNA relative to the surface of the histone octamer.

Question 42

DNA translocation generates _____
This loop is proposed to propagate on the surface of the histone octamer until it reaches the other end of the nucleosome DNA.

Answer 42

DNA translocation generates a loop of DNA that is released from the surface of the nucleosome near the site of translocation.
This loop is proposed to propagate on the surface of the histone octamer until it reaches the other end of the nucleosome DNA.

Question 43

The interaction of DNA with the ___ is dynamic. Like all interactions mediated by nonvalent bonds, the association of any particular region of DNA with the histone octamer is not ___.Critical for gene expression Binding of DNA-binding proteinsStudies of the ability of sequence- specific DNA-binding protein to bind nucleosomes suggest that _____.DNA sites ____ are the most accessible, and sites ____ are least accessible.

Answer 43

The interaction of DNA with the histone octamer is dynamicLike all interactions mediated by nonvalent bonds, the association of any particular region of DNA with the histone octamer is not permanent.Critical for gene expression Binding of DNA-binding proteinsStudies of the ability of sequence- specific DNA-binding protein to bind nucleosomes suggest that unwrapping of the DNA from the nucleosome is responsible for accessibility of the DNA.DNA sites closest to the entry and exit points are the most accessible, and sites closest to the midpoint of the bound DNA are least accessible.

Question 44

Specific DNA sequences can
position nucleosomes. Because DNA is __
during association with the nucleosome, DNA sequences that position nucleosomes are
intrinsically bent. A:T base pairs have an intrinsic
tendency to bend toward the __ which faces the histone
octamer. G:C base pairs have the opposite tendency.
Sequences that ___ with a periodicity of ~5bp will act as preferrednucleosome-binding sites

Answer 44

Specific DNAsequences can position nucleosomes Because DNA is bent severely during association with the nucleosome, DNA sequences that position nucleosomes are intrinsically bent.A:T base pairs have an intrinsic tendency to bend toward the minor groove, which faces the histone octamer. G:C base pairs have the opposite tendency. Sequences that alternate between A:T and G:C with a periodicity of ~5bp will act as preferred nucleosome-binding sites

Question 45

Many nucleosomes are not tightly positioned. Tightly positioned nucleosomes are most frequently found ___

Answer 45

Many nucleosomes are not tightly positioned. Tightly positioned nucleosomes are most frequently found at sites directing the initiation of transcription

Question 46

The significance of the location of nucleosomes
adjacent to important regulatory sequences has
led to the development of methods to monitor
the location of nucleosomes in cells. Determine the nucleosome position in cells: DNA with positioned nucleosome is resistant to ___, leaving a ~160-200b-region of DNA that is not cleaved

Answer 46

The significance of the location of nucleosomes
adjacent to important regulatory sequences has
led to the development of methods to monitor
the location of nucleosomes in cells. Determine the nucleosome position in cells: DNA with positioned nucleosome is resistant to micrococal nuclease digestion, leaving a ~160-200b-region of DNA that is not cleaved

Question 47

The amino-terminal tails of the histones are frequently modified. Specific modifications are associated
with histones involved in different cellular events.
Histone ____ acetylation is associated with the start sites of expressed genes.
Histone ___ acetylation marks newly synthesized H4 molecules that are ready to be deposited onto DNA as part of new nucleosome.
Histone ___ methylation is associated with expressed genes, while histone ___ methylation is associated with repressed genes.
Histone code theory: ____

Answer 47

The amino-terminal tails of the histones are frequently modified. Specific modifications are associated
with histones involved in different cellular events.
Histone H4 lysine (K) 8 and 16 acetylation is associated with the start sites of expressed genes.
H4K5 and H4K12 acetylation marks newly synthesized H4 molecule that are ready to be deposited onto DNA as part of new nucleosome.
H3K4, 36 or 79 methylation is
associated with expressed genes, while H3K9 or 27 methylation is associated with repressed genes.
Histone code theory: the histone tail modifications constitute a biological code that can be written, read and erased by specific proteins in the cells

Question 48

How does histone modification alter nucleosome function?
1. Acetylation and
phosphorylation each acts to___therefore reducing the ___.
2. Modification of the histone tails
affects the ability of nucleosome to ___.
A. The effect on association with nucleosome-bound DNA. Unmodified and methylated histone tails are thought to associate more tightly with __ than ___.
B. Modification of histone tails creates binding sites for chromatin-modifying enzymes.

Answer 48

How does histone modification alter nucleosome function? 1. Acetylation and phosphorylation each acts to
reduce the overall positive charge of the histone tail,
therefore reducing the affinity of the tails for the negative
charged backbones of DNAs.
2. Modification of the histone tails affects the ability of
nucleosome to form more repressive higher-order chromatin structure.
A.The effect on association with nucleosome-bound DNA. Unmodified and methylated histone tails are thought to associate more tightly with nucleosomal DNA than acetylated histone tails.
B. Modification of histone tails creates binding sites for chromatin-modifying enzymes.

Question 49

Protein domains in nucleosome-remodeling and
modifying complexes recognize modified histones
•Bromodomain-containing proteins: interact with ___
•Chromodomains: ___ interact with methylated histone tails.
•Sant domain-containing proteins: interact preferentially with the unmodified __
• HP1 protein: contains chromodomain, but only binds to the ___, but not other sites of histone modification.
TFIID ( a key component of the eukaryotic transcription machinery): contains a bromodomain. This domains directs the___, which is an additional way that histone acetylation contributes to the increased transcriptional activity of the associated DNA.
Chromodomains that recognize sites of histone methylation associated with ___ genes are found in several proteins that are important for the establishment of __, including HP1 and Polycomb proteins

Answer 49

Protein domains in nucleosome-remodeling and
modifying complexes recognize modified histones
•Bromodomain-containing proteins: interact with acetylated histone tails
•Chromodomain-Tudor domains and PhD finger containing proteins: interact with methylated histone tails.
•Sant domain-containing proteins: interact preferentially the unmodified histone tails
• HP1 protein: contains chromodomain, but only binds to the methylated H3K9, but not other
sites of histone modification.
TFIID ( a key component of the eukaryotic transcription machinery): contains a bromodomain. This domains directs the transcription machinery to the sites of histone
acetylation, which is an additional way that histon acetylation contributes to the increased transcriptional activity of the associated DNA.
Chromodomains that recognize sites of histone methylation associated with transcriptionally repressed genes are found in several proteins that are important for the establishment of heterochromatin, including HP1 and Polycomb proteins

Question 50

Nucleosome modification and remodeling work together to increase DNA accessibility

1. The DNA binding protein first recruits the___that modify the adjacent nucleosomes, increasing the accessibility of the associated DNA by locally converting the chromatin fiber from __ to the more accessible __.
2. The increased accessibility allows the binding of a second DNA-binding protein, which recruits ___.
3. Localization of the nucleosome-remodeling complex facilitates the ____, which allows the third DNA-binding site to be exposed. This could be the ___ protein at the start site of transcription.

Answer 50

Nucleosome modification and remodeling work together to increase DNA accessibility
1.The DNA binding protein first recruits the histone acetyltransferase that modify the adjacent nucleosomes, increasing the accessibility of the associated DNA by locally converting the chromatin fiber from 30-nm fiber to the more accessible 10-nm fiber.
2.The increased accessibility allows the binding of a second DNA-binding protein, which recruits nucleosome-remodeling complex.
3.Localization of the nucleosome-remodeling complex facilitates the sliding of the adjacent nucleosomes, which allows the third DNA-binding site to be exposed. This could be the
TATA-binding protein at the start site of transcription.

Question 51

Nucleosomes are assembled immediately after __.
Experiments using differentially labeled old and new histones: As the chromosome is replicated, histones that were associated with parental chromosome are differently distributed. __ are randomly transferred to one of the two daughter strands, but don’t enter the soluble pool of the __. Newly synthesized H3•H4 tetramers form the basis of __ in the ___strand.
H2A•H2B dimers are released in the ___, and compete with the new synthesized __ for binding to H2A•H2B dimers. On average, every second H3•H4 dimers will be derived from the __ chromosome. The H2A•H2B dimer are more likely from newly synthesized __.

Answer 51

Nucleosomes are assembled immediately after DNA replication
Experiments using differentially labeled old and new histones: As the chromosome is replicated, histones that were associated with parental chromosome are differently distributed. H3•H4 tetramers are randomly transferred to on of the two daughter strands, but don’t enter the soluble pool of the H3•H4 tetramers. Newly synthesized H3•H4 tetramers form the basis of nucleosome in the unoccupied strand.

H2A•H2B dimers are released in the soluble pool, and compete with the new synthesized H2A•H2B dimers for binding to H2A•H2B dimers. On average, every second H3•H4 dimers will be derived from the parental chromosome. The H2A•H2B dimer are more likely from newly synthesized protein

Question 52

Inheritance of parental H3•H4 tetramers facilitates the inheritance of chromatin states. As the chromosome replicates, the distribution of the parental H3•H4 tetramers results in the daughter chromosomes receiving ___. The ability of these modifications to recruit enzymes that perform the same modifications facilitates the propagation of___. The maintenance of such modification states is critical to maintain cell identity as cell replicate their DNA and divide.

Answer 52

Inheritance of parental H3•H4 tetramers facilitates the inheritance of chromatin states. As the chromosome replicates, the distribution of the parental H3•H4 tetramers results in the daughter chromosomes receiving the same modifications as the parent. The ability of these modifications to recruit enzymes that perform the same modifications facilitates the propagation of the modification to the two daughter chromosomes. The maintenance of such modification states is critical to maintain cell identity as cell replicate their DNA and divide.

Question 53

Chromatin assembly factors facilitate the assembly of nucleosomes. PNCA: ring-shaped sliding clamp protein. This factor forms a ring around the DNA duplex and is responsible for holding___during DNA synthesis. After the polymerase is finished, PCNA is released from Polymerase, but still encircles the DNA. Under this condition, __ associates with the released PCNA and assembles ___ preferentially on the PCNA-bound DNA. Thus by associating with a component of the DNA replication machinery, CAF-I is directed to assemble __ at the site of recent DNA replication

Answer 53

Chromatin assembly factors facilitate the assembly of nucleosomes PNCA: ring-shaped sliding clamp protein. This factor forms a ring around the DNA duplex and is responsible for holding DNA polymerase on the DNA during DNA synthesis. After the polymerase is finished, PCNA is released from Polymerase, but still encircles the DNA. Under this condition, CAF-I associates with the released PCNA and assembles H3•H4 preferentially on the PCNA-bound DNA.Thus by associating with a component of the DNA replication machinery, CAF-I is directed to assemble nucleosomes at the site of recent DNA replication