Iwafuchi 1

Question 1

What is the approximate length of DNA in a human cell?

Answer 1

2 meters

Question 2

What is the average diameter of a nucleus?

Answer 2

5-10 µm

Question 3

Besides being packaged efficiently, what is another requirement for DNA packaging?

Answer 3

It needs to be dynamic for transcriptional regulation.

Question 4

What is the diploid chromosome number in humans?

Answer 4

46 (23 pairs of chromosomes)

Question 5

The four core histones are _________.

Answer 5

H2A, H2B, H3, and H4

Question 6

What coincided with the emergence of core histones?

Answer 6

The emergence of eukaryotes

Question 7

How is bacterial DNA packaged compared to eukaryotic DNA?

Answer 7

Bacterial DNA is loosely packaged by histone-like proteins, while eukaryotic DNA is tightly packaged by core histone proteins

Question 8

Describe the ground state of gene regulation in bacteria versus eukaryotes.

Answer 8

Bacteria have a non-restrictive ground state, meaning genes are generally “on” unless repressed. Eukaryotes have a restrictive ground state, meaning genes are generally “off” unless activated.

Question 9

Which histone is considered the “linker” histone?

Answer 9

H1

Question 10

Which core histone exhibits the highest species conservation?

Answer 10

H4

Question 11

What structural motif do histone dimers form through?

Answer 11

A “helical handshake”

Question 12

Where is the histone fold located?

Answer 12

Within the globular domains of histones

Question 13

The N-terminal tails of core histones are unstructured, _____ amino acids long, and rich in ________-charged _______ and _______.

Answer 13

20-30, positively, lysine and arginine

Question 14

When does typical core histone synthesis occur?

Answer 14

During S phase

Question 15

What type of proteins catalyzes core histone assembly?

Answer 15

Chromatin assembly factors (CAFs)

Question 16

What is the function of the globular basic amino acids on the histone fold?

Answer 16

They bind tightly to the acidic DNA phosphodiester backbone

Question 17

Are core histone N-terminal tails well-defined by X-ray crystallography?

Answer 17

No, suggesting flexibility and no major role within the core nucleosome itself.

Question 18

Despite their lack of structure within the core nucleosome, what suggests the importance of core histone N-terminal tails?

Answer 18

They have highly conserved sequences in evolution.

Question 19

How many base pairs of DNA are in a nucleosome core particle?

Answer 19

~147 bp

Question 20

How many molecules of each core histone are in a nucleosome octamer?

Answer 20

2 molecules each of H2A, H2B, H3, and H4

Question 21

Describe the winding of DNA around the core octamer in a nucleosome.

Answer 21

DNA is wound in 1.7 superhelical turns.

Question 22

Describe the assembly of the histone octamer.

Answer 22

One tetramer of H3-H4 binds to DNA, followed by two H2A-H2B dimers.

Question 23

What amino acids are abundant in core histone tails?

Answer 23

Lysine (K) and arginine (R)

Question 24

What type of interactions are likely involved in contacts between adjacent nucleosomes?

Answer 24

Both histone-DNA and histone-histone interactions

Question 25

How do histone tails mediate inter-nucleosomal interactions?

Answer 25

Through charge-charge neutralization (acid-base electrostatic interactions)

Question 26

What effect does H1 binding have on the nucleosome?

Answer 26

It induces a more compact and rigid conformation.

Question 27

How does the H1 globular domain interact with DNA?

Answer 27

It interacts with core DNA on the dyad and with both DNA linkers.

Question 28

Where does the H1 C-terminal domain primarily associate?

Answer 28

With a single DNA linker

Question 29

What impact does H1 have on the nucleosome's symmetry?

Answer 29

It imparts a strong degree of asymmetry, likely influencing higher-order chromatin structure assembly.

Question 30

What is the name of the structural fold found in the globular domain of linker histones?

Answer 30

Winged helix fold

Question 31

How do both core and linker histones primarily interact with DNA?

Answer 31

Using positively charged arginine (R) and lysine (K) residues to interact with DNA backbone phosphates.

Question 32

Describe the structure of linker histones.

Answer 32

They have a tripartite structure consisting of a globular domain and intrinsically disordered tails.

Question 33

How does the ability to compact chromatin vary among H1 variants?

Answer 33

It varies; some have high, weak, or intermediate ability.

Question 34

What are the two major types of chromatin?

Answer 34

Heterochromatin and euchromatin

Question 35

Describe the condensation state of heterochromatin throughout the cell cycle.

Answer 35

Highly condensed

Question 36

What are some characteristic features of heterochromatin?

Answer 36

Found in centromeres, telomeres, and some other chromosomal locations. Typically composed of highly repetitive DNA sequences (tandem repeats).

Question 37

What typically happens to genes translocated into heterochromatic sequences?

Answer 37

They are transcriptionally inactivated.

Question 38

What is the state of the inactive X chromosome in female somatic cells?

Answer 38

It is heterochromatic and highly condensed.

Question 39

When does euchromatin become highly condensed?

Answer 39

Only at metaphase

Question 40

Describe the condensation level of euchromatin during interphase.

Answer 40

Intermediate level of condensation

Question 41

What is the transcriptional state of genes within euchromatin?

Answer 41

They can be transcriptionally active or inactive.

Question 42

What are the components of chromatin?

Answer 42

DNA + core histones = nucleosomes + linker histone H1 (closes chromatin)

Question 43

What cellular phases does interphase comprise?

Answer 43

G1, S, and G2 phases

Question 44

What is the state of chromosomes during interphase?

Answer 44

Relatively decondensed

Question 45

What phases are included in the M phase (mitosis)?

Answer 45

Prophase, metaphase, anaphase, telophase, and cytokinesis

Question 46

When do chromosomes reach their maximum compaction?

Answer 46

At metaphase

Question 47

What are the two important functional landmarks of chromosomes?

Answer 47

Centromere (links sister chromatids) and telomeres (chromosome ends)

Question 48

Where are A-compartment domains positioned within chromosome territories?

Answer 48

Towards the nuclear interior

Question 49

All somatic cell types within the body have the same set of ______ but exhibit unique patterns of chromatin and epigenetic states, which influence cell-type-specific gene expression profiles.

Answer 49

genes

Question 50

___________ determine the timing, location, and level of promoter activation. They're crucial for cell-type specific gene regulation.

Answer 50

Transcription factors at the enhancer

Question 51

The human haploid genome (a single set of chromosomes) comprises _______ bp

Answer 51

3E9

Question 52

Length of DNA in an average human body (i.e., all cells counted) is estimated at ______ miles (6,000 times the distance of the moon from the Earth)

Answer 52

5E9

Question 53

Bacteria DNA has ______ x compaction, while Eukaryotic DNA has __________ x compaction.

Answer 53

1,000; 10,000

Question 54

Bacteria DNA is _________ (tightly/loosely) packed by histone-like proteins, while Eukaryotic DNA is __________ (tightly/loosely) packed by core histones.

Answer 54

loosely, tightly

Question 55

There are ________ amino acids in H4.

Answer 55

102

Question 56

There are _______ amino acids in H3.

Answer 56

135

Question 57

There are _________ amino acids in H1.

Answer 57

220

Question 58

H4 has an extremely high degree of conservation amongst species, while H1 has a _______ degree of conservation.

Answer 58

moderate

Question 59

The ___________ in core histones (where the histone fold is situated) contain many buried hydrophobic amino acids, but also many positively charged residues at the surface that help dictate DNA binding geometry around the nucleosome.

Answer 59

globular domains

Question 60

The process of octamer assembly is catalyzed by chaperone proteins called ____________. These are essential adjuncts to the process, since otherwise jumbled protein aggregates will form readily.

Answer 60

chromatin assembly factors (CAFs)

Question 61

Typical core histone synthesis occurs during _______ phase, when DNA is being replicated.

Answer 61

S phase

Question 62

The “globular” ______ (basic/acidic) amino acids (situated on the perimeter of the protein disc) are involved in binding tightly to the ______ (basic/acidic) DNA phosphodiester backbone

Answer 62

basic, acidic

Question 63

A core nucleosome has approximately _____ bp of dsDNA wrapped around it.

Answer 63

147

Question 64

Assembly of octamer proceeds by binding of one ________ (tetramer/dimer) of H3-H4 to DNA followed by two H2A-H2B _______ (tetramers/dimers).

Answer 64

tetramer, dimers

Question 65

Core histone tails are extremely rich in ________ (amino acid) and _______ (amino acid), meaning they are highly _______ (negatively/positively) charged.

Answer 65

lysine, arginine, positively

Question 66

True or False: In inter-nucleosomal interactions, histone-histone interactions are likely to be more important than histone-DNA interactions.

Answer 66

True

Question 67

H1 binding induces the nucleosome to adopt a more _____________ conformation.

Answer 67

compact and rigid

Question 68

The H1 globular domain interacts with ________ on the dyad and with both DNA linkers.

Answer 68

core DNA

Question 69

The H1 C-terminal domain associates primarily with a single __________.

Answer 69

DNA linker

Question 70

H1 imparts a strong degree of ___________ (symmetry/asymmetry) to the nucleosome, which is likely to influence the assembly and architecture of higher-order chromatin structures. The linker histone H1 also stabilizes a ______ nucleosome conformation.

Answer 70

asymmetry, compact

Question 71

Linker histones has ____partite structure.

Answer 71

tri

Question 72

True or False: Linker histone H1 molecules exist in many variant forms.

Answer 72

True

Question 73

True or False: Genes within euchromatin can be transcriptionally active or inactive.

Answer 73

True

Question 74

Interphase comprises the G1, S and G2 phases of the cell cycle – chromosomes are relatively ____________ (condensed/decondensed) during these stages

Answer 74

decondensed

Question 75

Chromosomes contain two important functional landmarks – the ___________ that links sister chromatids, and _________ (chromosome ends).

Answer 75

centromere, telomeres

Question 76

Gene expression and DNA replication occur in the cell cycle __________.

Answer 76

interphase

Question 77

True or False: Individual chromosomes occupy distinct territories.

Answer 77

True

Question 78

LADs stand for ______.

Answer 78

Lamina-associated domains

Question 79

TADs stand for ________.

Answer 79

Topologically-associating domains

Question 80

At smaller scales, chromatin is organized into insulated spatial neighborhoods referred to as _____ or loop domains.

Answer 80

TADs