10-nm fiber
The "beads-on-a-string" form of chromatin, in which DNA is wrapped around nucleosomes.
30-nm fiber (solenoid)
A structure of chromatin in which histone 1 (H1) partially condenses chromatin fibers into a coiled form.
300-nm fiber
A structural state of chromatin in which chromatin fibers are looped and condensed.
acrocentric chromosome
A eukaryotic chromosome in which the centromere is very near one end. Forms a chromosome with a long and short arms of distinctly different lengths.
chromatin
The complex of nucleic acids and proteins that compose eukaryotic chromosomes.
chromatin remodeling
Processes that modify the structure or composition of chromatin. Usually associated with alterations of nucleosome binding to DNA and affecting the regulation of gene transcription.
chromosome arms
(long arm-q arm; short arm-p arm) The segments of eukaryotic chromosomes between the centromere and the telomeres.
chromosome banding (Giemsa banding-G banding)
A group of laboratory methods that stain eukaryotic chromosomes to reveal distinctive patterns of light and dark bands. Chromosome banding by Giemsa staining produced standardized patterns for different chromosome of selected species.
chromosome scaffold
Composed of numerous nonhistone proteins, the superstructure of eukaryotic chromosomes.
chromosome territory
The region within a nucleus occupied by a particular chromosome during interphase.
constitutive heterochromatin
Chromosome regions containing chromatin that is always densely compacted. Usually containing highly repetitive DNA sequences.
core DNA
The approximately 146 base pairs of eukaryotic DNA that wrap each nucleosome.
epigenetic marks (epigenetic modifications)
A collection of chemical marks and modifications, such as acteylation and methylation of histone proteins, that are functional in chromatin remodeling.
euchromatin (euchromatic region)
Chromosome regions containing chromatin that is not densely compacted. Most expressed genes are located within euchromatic regions of chromosomes.
E(var) mutations
Mutations that enhance position effect variegation in Drosophila. Mutated genes produce proteins that are active in chromatin remodeling.
facultative heterochromatin
Heterochromatic chromosome regions whose level of compaction can vary. Often contains repetitive DNA, but may also contain some expressed genes.
fluorescent in situ hybridization (FISH)
A laboratory method for identifying genes or DNA sequences using molecular probes labeled with a compound that can emit fluorescent light upon excitation.
heterochromatin (heterochromatic region)
A chromosome region containing densely compacted chromatin and few, if any, expressed genes.
histone proteins (H1, H2A, H2B, H3, H4)
Five proteins encoded by a gene family that form octameric nucleosomes (H2A, H2B, H3, and H4) and adhere to DNA to condense chromatin (H1).
in situ hybridization
A laboratory method for hybridizing a molecular probe to a DNA sequence or a gene on an intact chromosome.
interchomosomal domain
Open spaces between chromosome domains in the interphase nucleus.
karyotopye
A digital of analog photograph of chromosomes arranged by conventional chromosome numbering.
linker DNA
DNA between nucleosomes in the 10-nm fiber structure of chromatin.
matrix attachment region (MAR)
Portions of the chromosome scaffold to which loops of chromatin are attached.
metacentric chromosome
A chromosome with a centrally located centromere that produces long and short arms of approximately the same length.
negative supercoiling
Twisting of the DNA duplex in the direction opposite to the turns of the double helix.
nonhistone proteins
Numerous nuclear proteins that are not histones associated with chromosomes.
nucleoid
The region of bacterial and archaeal cells (or mitochondria or chloroplasts) where the main chromosome resides.
nucleosome
An octameric protein complex composed of two polypeptides each of histones H2A, H2B, H3, and H4, around which DNA wraps in chromatin.
position effect variegation (PEV)
The observation in Drosophila of a specific type of mutation producing variegation of eye color due to the abnormal positioning of the w (white) gene for eye color.
positive supercoiling
Superhelical twisting of DNA.
radial loop-scaffold model
A model of chromatin structure that predicts rosettes of looped chromatin on a chromosome scaffold.
small nucleoid-associated proteins
In bacterial DNA, small proteins localized to the nucleoid and associated with the main chromosome.
solenoid structure
30-nm fiber
structural maintenance of chromosomes (SMC) proteins
A category of bacterial proteins localized to the nucleoid and associated with the main chromosome.
submetacentric chromosome
A chromosome with a centromere located near the midpoint that produces long and short arms of different lengths.
Su(var) mutations
Mutations that suppress position effect variegation in Drosophila. Mutated genes produce proteins that are active in chromatin remodeling.
telocentric chromosome
A chromosome with a centromere located at one end, producing a long arm only.
Which of the following statements best describes bacterial genome organization?
Bacterial genomes may consist of a single circular chromosome or multiple chromosomes that may be linear or circular.
What is the primary mechanism of chromosome compaction in E. coli?
Proteins organize the chromosome into loops that are supercoiled to form the nucleoid.
Which of the following best describes the overall composition (by mass) of eukaryotic chromatin?
50% DNA, 50% protein
What is the primary function of histone H1?
To stabilize the 30-nm solenoid
Which of the following statements about the relationship between histone modification and chromatin packaging is true?
Methylation of histone tails generally results in tighter packaging of chromatin.
Which type of chromosome structure is characterized by the centromere position very near the end of the chromosome with the short arm composed of highly repetitive (satellite) DNA?
Acrocentric
Which type of DNA produces a light band when treated with Giemsa stain?
Euchromatin; Euchromatin contains actively transcribed genes. It is not highly condensed and therefore does not bind significant amounts of Giemsa stain.
What is a chromosome territory?
A small region of the interphase nucleus that is occupied by a single chromosome, or portion thereof.
What process is responsible for position effect variegation?
Inactivation of a gene due to its incorporation in a heterochromatic region of the chromosome.
What is a bacterial nucleoid?
is the location of the bacterial chromosome within a bacterium.
What is a bacterial plasmid?
is a circular DNA molecule that is distinct from the chromosome.
What is the relative difference you expect between the levels of chromosome condensation in interphase and in metaphase?
Interphase chromosomes will be less condensed than metaphase chromosomes.
Where is it more likely to find the DNA sequence encoding the digestive enzyme amylase?
euchromatic region
Histone proteins
bind to DNA to form the nucleosome core particles.
Nucleosomes
are complexes containing two H2A/H2B dimers and two H3/H4 dimers, around which 146 bp of DNA are wrapped.
CEN sequences
are located at centromeres.
G bands
are darkly stained regions of compacted chromosomes (heterochromatin) that have been stained with Giemsa.
Euchromatin
is the relatively less condensed region of chromosomes.
Heterochromatin
is the relatively more condensed region of chromosomes.
Epigenetic modification
promotes the formation of either euchromatin or heterochromatin.
Chromosome territories
are the regions of the nucleus occupied by a particular chromosome.
Nucleoids
are the region of a bacterial cell that contains the bacterial chromosome.
What are the two principal mechanisms of bacterial DNA compaction?
supercoiling; folding into loops
These are extra-chromosomal DNA molecules that carry nonessential genes
plasmids
Bacterial and archaeal chromosomes are densely packed to form a small region called the
nucleoid
Bacterial and archaeal chromosomes are organized into
series of tight loops
Why are bacterial/archaeal chromosomes organized into series of tight loops?
Efficient packaging
Two methods of bacterial chromosome compaction
proteins organize DNA into loops that pack the chromosome into nucleoid AND supercoiling
Participates in DNA bending that contributes to folding and condensation of chromosomes
small nucleoid-associated proteins
These attach directly to the DNA, holding it in coils or V-shapes to form large nucleoprotein complexes
structural maintenance of chromosome (SMC)
Supercoiling: the least twisted
relaxed circle
Supercoiling: the most tightly twisted
highly supercoiled
Purpose of highly supercoiled form of chromosome?
Occupies less space in nucleoid
Occurs in most bacteria and archaea and twists DNA in opposite direction to helical twist
negative supercoiling
Twists the DNA in the same direction as the double helix
positive supercoiling
Positive supercoiling occurs in bacteria?
No, in some archaea
Partially unwinds supercoild DNA to relieve torsional stresses that could result from "overwinding
topoisomerases
Eukaryotic DNA and associated proteins of a chromosome are called
chromatin
Eukaryotes chromatin composition: each chromosome is approximately
half DNA/half protein
Eukaryotes chromatin composition: the proteins are
half histone proteins/ half nonhistone proteins
Eukaryote histones: how many histone proteins?
5
Eukaryote histones: histone proteins are highly ______ among eukaryotes
conserved
Eukaryote histones: around 146 bp of DNA wrap around each histone octamer to form
nucleosome
Eukaryote histones: two molecules each of H2A/H2B/H3/H4 form an
octamer
Nucleosome assembly: wrapping of DNA around nucleosome compacts it how much
sevenfold
Euk. Chromatin structure: the DNA wrapped around the core particle is called
core DNA
Euk. Chromatin structure: the core particle is
histone octamer
Euk. Chromatin structure: least condensed state show a
10 nm fiber
Euk. Chromatin structure: the 10-nm fiber is referred to as
beads-on-a-string" morphology
Euk. Chromatin structure: what are the "beads
nucleosomes
Euk. Chromatin structure: the variable-length "string" between nucleosomes is
linker DNA
Are 10-nm fibers observable under normal cellular conditions?
No
What is observed under normal cellular conditions?
30 nm fiber
The 30-nm fiber forms when the 10-nm fiber coils into a
solenoid structure
What stabilizes the solenoid
histone (H1)
When does chromatin exist as 30-nm fiber (or more condensed state)
during interphase
Maximal condensation of chromatin structure occurs during
metaphase of mitosis
Interphase chromosomes have variably sized loops of 30-nm that form
300-nm fiber
Chromosome shape depends on the
chromosome scaffold
What composes chromosome scaffold?
Filamentous, nonhistone proteins
Chromatin loops of 20-100 kb are anchored to the chromosome scaffold by nonhistone proteins at sites called
matric attachment regions (MARs)
What model suggests that loops gather into "resettes" and further compressed by nonhistone proteins?
Radial loop-scaffold model
What state of mitosis is chromatin compacted 250 fold (compared to 300 nm fiber)
metaphase
What allows for efficient separation of chromosomes at anaphase?
Chromosome compaction
The chromatin loops formed during condensation play a role in
regulation of gene expression
Active transcription takes place in segments of loops ____ from MARs
distant
Which loops have more active transcription?
Larger loops
Most nucleosomes present after replication are assembled from
partially old nucleosome components and partially from new histones
Nucleosomes must be displaced to expose promoter and other regulatory sequences
chromatin remodeling
Why does chromatin remodeling occur?
Expose regulatory sequences (ex. Promoter)
Chemical modifications to histones in nucleosomes are
epigenetic marks or epigenetic modifications
What does epigenetic marks control?
How tight DNA/nucleosomes bind together
Where do modifiations to histones take place
N-terminus of protein
Epigenetic modifications consist of addition or removal of
chemical groups
This chemical group tightens DNA packaging and reduces transcriptional activity
methyl group
This chemical group loosens packaging and increases transcription
acetyl group
Tight DNA =
reduced transcription activity
Loose DNA =
increased transcription activity
How are epigenetic modifications of histones transmitted?
Cell division/reproduction
What provides a mechanism for maintaining the modifications and passing them to daughter cells?
Retention of old histones during DNA replication
Epigenetic marks affect
gene transcription
Epigenetic marks do not affect
DNA sequence
Chromosome condensation reaches a max at
metaphase of mitosis
During metaphase cytogeneticists can distinguish chromosomes microscopically based on
size, shape and banding pattern
What appears light or dark when chromosomes are treated with specific dyes and stains?
Chromosome bands
What divides chromosomes into chromosomes arms
centromeres
Chromosome short arm is called
p arm
Chromosome long arm is called
q arm
Chromosome shapes are named based on
centromere position
What determines the relative sizes of the chromosome arms
centromeres
The centromere is near the middle of the chromosome
metacentric
The centromere is btw center and the tip of the chromosome
submetacentric
The centromere is close to one end of the chromosome
acrocentric
The centromere is at the tip of the chromosome and there is no p arm
telocentric
An ordered photographic display of a complete set of chromosomes for a species
karyotype
Karyotypes: The chromosomes are grouped into
homologous pairs in big to small
Karyotypes: what chromosome is ID. Separately
sex chromosome
Karyotypes: Dye staining shows
distinctive banding patterns
Allows cytogeneticists to id each chromosome in a karyotype
chromosome banding
What is used to produce banding patterns in karyotypes?
Different stains and dyes
The standard for human chromosome banding is
Giemsa banding
Why is Giemsa banding the standard?
Distinct and reproducible patterns
Karyotypes: Regions that contain actively expressed genes and are less condensed during interphase are
euchromatin
Karyotypes: Regions that remain condensed in interphase and contain many fewer expressed genes are called
heterochromatin
Type of Heterochromatin: exhibits variable levels of condensation, related to levels of transcription of resident genes
facultative heterochromatin
Type of Heterochromatin: is permanently condensed, found prominently in centromeres and telomeres, and composed primarily of repetitive DNA sequences
constitutive heterochromatin
Repetitive DNA sequences in centromeres facilitate binding of
kinetochore proteins and spindle
Carbon and Clarke found that the 16 centromeres of S. cerevisiae each had slightly different sequences called
CEN sequences
CDE I is ___ bp
8 bp
In consensus of CDE I: RTCARTG what is R
purine
CDE II is varied in ____ and at least 90% _____
length; A-T
CDE II is the site of
microtubule attachement
CDE III is ___ bp
26 bp
CDE III is composed mainly of
A-T pairs
Centromeric DNA sequences of eukaryotes are
highly repetitive/constitutively heterochromatic
What takes place of histone H3 in centromeric nucleosomes?
CENP-A
Where on CENP-A allows the binding of kinetochore proteins to the centromere?
N-terminal tail
Uses molecular probes to detect their target sequences?
In situ hybridization
In situ hybridization molecular probes are labeled with
fluorescence or radioactivity
Older (1st generation) methods of In situ hybridization used nucleotides labeled
32P
New gen. in situ hybridization utilizes this as nucleotide label
fluorescent labels
Benefit of fluorescent labels
better resolution
Uses molecular probes labeled with compounds that emit fluorescent light when excited by UV/visible light
fluorescent in situ hybridization
Chromatin structure influences
gene transcription
Prominent diff. btw eukaryote and bacterial genome
chromatin
How many diff. fluorophores available for human chromosome
24
Each fluorophores is unique to
each chromosome
Are chromosome uniformly distributed within a nucleus
No
First observed chromosome distribution was not uniform within the nucleus
Boveri
Suggested that the variation in position might be related to gene activity
Boveri
Partitioning of chromosomes into specific regions
chromosome territories
Showed that chromosomes are partitioned into specific regions during interphase
Cremer and Cremer
Once confined to a territory a chromosome does not leave until
M phase is initiated
Chromosomes appear to be ____ in their territories by their centromeres
anchored
During transcription and DNA replication chromosomes are ____ within their territories
active
Regions between territories that act as channels for movmt of proteins,enzymes, and RNA molecules
interchromosomal domains
Located near the center of the nucleus
early replicating parts of chromosome
Located near the periphery of the nucleus
late replicating parts of chromosome
Transcriptionally active portions of chromosomes thought to be nearer to interchromosomal domains due to
Access to needed proteins/enzymes AND faster dispersal of RNA transcripts
What regulates access to DNA by proteins for replication, transcription, recombination, and repair?
Changes in level of compaction
In drosophila illustrates the effect of chromatin compaction on gene expression
position effect variegation (PEV)
Muller noticed that the X chromosomes of flies with variegated eye color had undergone
inversion
What determines whether or not the relocated white gene will be expressed?
Stopping point of heterochromatic spread
Occurrence of PEV shows: Gene expression can be _______ by the gene's chromosomal position
silenced
Occurrence of PEV shows: Silencing is a feature of _____ _____ that can be transmitted from one generation to the next.
Chromatin structure
Genetic analysis of eukaryotic genomes shows that PEV is
widespread
What led to id. of proteins that play a role in establishing and maintaining chromatin structures?
Mutations modifying PEV
Enhancers of position-effect variegation, increase of enhance the appearance of the mutant white phenotype in flies with a variegating allele of the white gene
E(var) mutation
E(var) encourage the spread of ____ beyond its normal boundaries
heterochromatin
These mutations produce a greater number of eye cells lacking pigment
E(var) mutations
Suppressors of position-effect variegation, increase or enhance the appearance of the mutant white phenotyple in flies with a variegating allele of the white gene
Su(var) mutations
This mutation encourages the spread heterchromatin beyond its normal boundaries
E(var) mutation
This mutation restricts the spread of heterochromatin or interfere with its function
Su(var)s mutations
These mutations produce a greater number of pigmented eye cells
Su(var) mutations
Red patches are produced by cells in which w+ is transcribed, an white patches in which w+ is inactivated by heterochromatin spread
variegated eye
Mutation block efficient formation of heterochromatin and leave most cells with active w+ transcription
Su(var) mutations
Mutations enhance heterochromatin formation and restrict w+ expression to small patches
E(var) mutations
Chromatin is static/dynamic
dynamic
What is associated with gene expression
chromatin
Important feature of Epigenetic Modification: Alters what structure
chromatin
Important feature of Epigenetic Modification: Transmissible?
Yes, during cell division
Important feature of Epigenetic Modification: Permanent?
No, reversible
Important feature of Epigenetic Modification: Directly associated with
gene transcription
Important feature of Epigenetic Modification: Alters DNA sequence?
No
The most common epigenetic modifications of histones in heterochromatin regions
methylation of lysine 9 of H3
The absence of ____ interferes with heterochromatin formation and suppresses variegation
HP-1