Ch. 10 Learnsmart Chromosome Organization & Molecular Structure

D

A bacterial chromosome typically contains (A) a few thousand genes (B) one origin of replication (C) some repetitive sequences (D) all of the above

C

A chromosome territory is a region (A) along a chromosome where many genes are clustered (B) along chromosome where the nucleosomes are close together (C) in a cell nucleus where a single chromosome is located (D) in a cell nucleus where multiple chromosomes are located

Eukaryotic

A chromosome that is linear, millions of bp long, has a centromere, two telomeres, and multiple origins of replication is from what type of cell?

30-nm fiber

A compact structure of associated nucleosome units that is 30 nm in diameter => Shortens the total length of DNA another seven-fold => Conformation has proven difficult to determine b/c the conformation of DNA may be substantially altered when extracted from living cells

Chromosome territory

A discrete region in the cell nucleus occupied by a single chromosome => It is non-overlapping

Nucleosome

A double-stranded segment of DNA wrapped around an octamer of histone proteins that is the repeating structural unit w/in eukaryotic chromatin • Each octamer has eight histone subunits => Two copies each of four different histone proteins => DNA is negatively supercoiled over surface of octamer, making 1.65 negative superhelical turns around a histone octamer => Amount of DNA required to wrap around the histone octamer is 146 or 147 bp • At its widest point, a single _________ is about 11 nm in diameter

Nuclear matrix (scaffold)

A group of proteins that anchor the loops found in eukaryotic chromosomes • Consists of two parts: (1) Nuclear lamina: collection of filaments that line the inner nuclear membrane => These filaments are composed of intermediate filament proteins (2) Internal nuclear matrix: connected to the nuclear lamina and fills the interior of the nucleus => Hypothesized to be an intricate fine network of irregular protein filaments w/ many other proteins bound to them => May still be intact even when the chromatin is extracted from the nucleus => Protein composition is very dynamic and complex, consisting of dozens or perhaps hundreds of different proteins ==> Protein composition varies depending on species, cell type, and environmental conditions

Kinetochore

A group of proteins that assemble just before and during the very early stages of mitosis and meiosis that link the spindle apparatus to the centromere during meiosis and mitosis , ensuring the proper segregation of the chromosomes to each daughter cell

Nucleus

A membrane-bound organelle in eukaryotic cells where the linear sets of chromosomes are found

Intron

A non-coding sequence of DNA that is found w/in a protein coding gene is called a(n)

Scaffold-attachment regions (SARs)

A site in the chromosomal DNA that is anchored to the nuclear scaffold => Bind to specific proteins in the nuclear matrix, thus forming chromosomal loops => Also called matrix-attachment regions (MARs)

Retroelement

A type of transposable element that is transcribed into RNA, copied into DNA, and inserted into the genome => The AluI highly repetitive sequence is an example of this

Thousands

A typical eukaryotic gene ranges in size from several thousands to tens of ______ of base pairs

A, C, B

As a cell proceeds through mitosis, the amount of cohesin bound to sister chromatids changes. Place the descriptions of cohesin binding in order from earlier in mitosis at the top to later in mitosis (anaphase) at the bottom: (A) Cohesins along the chromatid arms (B) Cohesins cleaved by separase and degraded (C) Only some cohesin bound at centromeric region

One microdomain is 10,0000 bp. One bp is 0.34 nm, which equals 0.00034 µm. You multiply the two together: (10,000)(0.00034 µm) = 3.4 µm

As described in Ch. 9, 1 bp of DNA is ~0.34 nm in length => A bacterial chromosome is about 4 million bp in length => The dimensions of the cytoplasm of a bacterium, such as E. coli are roughly 0.5 µm wide and 1.0 µm long A microdomain is a loop that contains about 10 kb of DNA => If such a loop was stretched out linearly, how long (in µm) would the DNA be?

Structural maintenance of chromosomes (SMC) proteins

DNA-binding proteins found in both the nucleoids of bacterial cells and the nuclei of eukaryotic cells that tether segments of DNA to each other

Circumference = piD => 3.4 µm = piD => D = 1.1 µm

As described in Ch. 9, 1 bp of DNA is ~0.34 nm in length => A bacterial chromosome is about 4 million bp in length => The dimensions of the cytoplasm of a bacterium, such as E. coli are roughly 0.5 µm wide and 1.0 µm long If a bacterial microdomain was circular, what would be its diameter? (Note: Circumference = pi*D, where D is the diameter of the circle)

Circular

Bacterial chromosomal DNA is usually ______, though some bacteria have linear chromosomes

Nucleoid

Dark-staining region of bacterial cell that contains the highly compacted chromosome => Bacteria may have one to four identical chromosomes per cell depending on growth conditions and phase of cell cycle => Each chromosome is found w/in its own distinct ___________ => Unlike a eukaryotic nucleus, it is not a separate cellular compartment surrounded by a membrane => DNA inside of it are in direct contact with cytoplasm of cell

Tandem arrays (tandem repeats)

Clusters of highly repetitive very short sequences that are repeated many times in a row => In Drosophila, 19% of chromosomal DNA consists of highly repetitive sequences found in these

Nuclear lamina

Collection of filaments that line the inner nuclear membrane and make up part of the nuclear matrix or nuclear scaffold > These filaments are composed of intermediate filament proteins

Topoisomers

DNA conformations that differ with regard to supercoiling => Negative supercoils from Left-handed turn (underwinding) and positive supercoils from right-handed turn (overwinding) are __________ of each other

D

DNA gyrase (A) promotes negative supercoiling (B) relaxes positive supercoils (C) cuts DNA strands as part of its function (D) does all the above

The solenoid model depicts the nucleosomes in a repeating, spiral arrangement, whereas the zigzag model depicts a more irregular and dynamic arrangement of nucleosomes

Describe the distinguishing features of the solenoid and zigzag models

The radial loop domains become closely compacted

Describe what structural changes convert a chromosomal region that is 300 nm in diameter to one that is 700 nm in diameter

Genome

Entire complement of genetic material in an organism or species

DNA gyrase

Enzyme discovered by Gellert that introduces negative supercoils into DNA using energy from ATP and that can relax positive supercoils when they occur => Contains four subunits (two A and two B subunits) => A.k.a topoisomerase II

Topoisomerase I

Enzyme that relaxes negative supercoils => Binds to negatively supercoiled region and introduces break in one of DNA strands => After one DNA strand has been broken, the DNA molecule rotates to relieve the tension that is caused by negative supercoiling => This rotation relaxes negative supercoiling => The broken strand is then repaired => The competing actions of DNA gyrase and this enzyme govern the overall supercoiling of bacterial DNA

Replication

Eukaryotic chromosomes contain three types of regions required for chromosomal _________ and segregation: (1) origins of replication (2) centromeres (3) telomeres

Segregation

Eukaryotic chromosomes contain three types of regions required for chromosomal replication and ___________: (1) origins of replication (2) centromeres (3) telomeres

Unique (nonrepetitive) sequences

Sequences found once or a few times w/in a genome => Protein-encoding genes are typically these types of sequences of DNA => Make up roughly 41% of the entire human genome (1) Protein-encoding regions of genes (2%) (2) Introns (24%) (3) _____ regions that are not found w/in genes (15%)

DNA super-coiling

Formation of additional coils in DNA due to twisting forces

Protein-encoding genes (structural genes)

Genes that produce mRNA and encode polypeptides => Make up the majority of bacterial DNA

Histone proteins

Groups of proteins that consist of globular domains and a flexible, charged amino terminus called an amino terminal tail => Very basic proteins b/c they contain a large number of positively charged lysine and arginine amino acids => Arginines play a major role in binding to the DNA by forming electrostatic & H-bonding interactions w/ the phosphate groups along the DNA backbone

Heterchromatin

Highly compacted regions of chromosomes where DNA is usually transcriptionally inactive => 30-nm fiber radial loop domains are compacted further than in euchromatin => Most abundant in the centromeric regions of the chromosome and, to a lesser extent, in the telomeric regions

H1

Histone protein that plays a role in the packaging and compaction of nucleosomes

Two

How many nucleoids are in this bacterial cell?

B

In Noll's experiment to test the beads-on-a-string model, exposure of nuclei to a low concentration of DNase I resulted in (A) a single band of DNA w/ a size of ~200 bp (B) several bands of DNA in multiples of 200 bp (C) a single band of DNA w/ a size of 100 bp (D) several bands of DNA in multiples of 100 bp

C

In a nucleosome, what is the nature of the chemical attraction b/w the histone proteins & the DNA? (A) The acidic histone proteins are attached to the negatively charged DNA molecule (B) The negatively charged hsitone proteins are attracted to the positively charged DNA molecule (C) The basic histone proteins are attached to the phosphate groups along the DNA backbone (D) The negatively charged histone proteins are attracted to the negatively charged DNA molecule

ATP is needed so the DNA in the upper jaws can pass through the break in the DNA and pass through the region of the lower jaws

In your own words, describe the step that requires the use of ATP

E

The chromosomes of eukaryotes typically contain (A) a few hundred to several thousand different genes (B) multiple origins of replication (C) a centromere (D) telomeres at their ends (E) all the above

It's probably a little too big to fit inside an E. coli. Keep in mind that a single chromosome contains 400 to 500 microdomains. NAPs and supercoiling are needed to make the loops much more compact so that a single chromosome can occupy a nucleoid w/in the bacterial cell

Is the diameter of the circular loop calculated in part B small enough to fit inside a bacterium?

Euchromatin

Less compacted regions of chromosomes where DNA may be transcriptionally active => the 30-nm fiber forms radial loop domain

Microdomains

Loops of DNA emanating from the central core of the bacterial chromosome that are typically 10 kbp in length => An E. coli chromosome is expected to have about 400-500 of them => Their lengths and boundaries are thought to be dynamic

Radial loop domains

Loops, often 25,000 to 250,000 bp in size, into which DNA is organized into the nuclear matrix and which are anchored to it at matrix attachment regions (MARs)

D

Mechanisms that make the bacterial chromosome more compact include (A) the formation of micro- and macro-domains (B) DNA supercoiling (C) Crossing over (D) Both a and b

Cohesion

Multiprotein complex that facilitates the alignment of sister chromatids

Condensin

Multiprotein complex that plays a critical role in condensation of interphase chromosomes to become metaphase chromosomes

B

Negative supercoiling may enhance activities like transcription and DNA replication b/c it (A) allows the binding of proteins to the major groove (B) promotes DNA strand separation (C) makes the DNA more compact (D) causes all the above

Introns

Noncoding intervening sequences => Their presence in more complex eukaryotes such as mammals and flowering plants, is why their protein-encoding genes tend to be much longer => Size ranges from <100 bp to more than 10,000 bp

C, E, A, B, D

Order the levels of chromatin compaction from the least condensed at the top of the list to the most condensed at the bottom of the list (A) Formation of the 30-nm fiber (B) Formation of radial loops (C) DNA double helix (D) Heterochromatin in mitotic chromosomes (E) Wrapping DNA around histones

Eukaryotic

Organization of _________ chromosomes: • Usually linear • Occur in sets. Many species are diploid, which means that somatic cells contain 2 sets of chromosomes • A typical chromosome is tens of millions to hundreds of millions of base pairs in length • Genes are interspersed throughout the chromosome. A typical chromosome contains b/w a few hundred and several thousand different genes • Each chromosome contains many origins of replication that are interspersed about every 100,000 base pairs • Each chromosome contains a centromere that forms a recognition site for the kinetochore proteins • Telomeres contain specialized sequences located at both ends of the linear chromosome • Repetitive sequences are commonly found near centromeric and telomeric regions, but they may also be interspersed throughout the chromosome

Bacterial

Organization of sequences in _________ chromosomal DNA • Most, but not all, bacterial species contain circular chromosomal DNA • Most bacterial species contain a single type of chromosome, but it may be present in multiple copies • A typical chromosome is a few million base paris in length • Several thousand different genes are intersperse throughout the chromosome. The short regions b/w adjacent genes are called intergenic regions • One origin of replication is required to initiate DNA replication • Repetitive sequences may be interspersed throughout the chromosome

Gyrase

Overview of DNA ______ function: (1) Step One: => DNA binds to lower jaws (2) Step 2: => DNA wraps around the A subunits in a right-hand direction (3) Step 3: => Upper jaws clamp onto DNA (4) Step 4: => DNA held in lower jaws is cut. => DNA held in upper jaws is released and passes downward through the opening in the cut DNA. => This process uses 2ATP molecules (5) Step 5: => Cut DNA is ligated back together and the DNA is released from DNA gyrase

Internal nuclear matrix

Part of the nuclear matrix/scaffold that is connected to the nuclear lamina and fills the interior of the nucleus => Hypothesized to be an intricate fine network of irregular protein filaments w/ many other proteins bound to them => May still be intact even when the chromatin is extracted from the nucleus => Protein composition is very dynamic and complex, consisting of dozens or perhaps hundreds of different proteins ==> Protein composition varies depending on species, cell type, and environmental conditions

Facultative heterochromatin

Refers to chromatin that can occasionally interconvert b/w heterochromatin and euchromatin => Example occurs in mammals where one of two X chromosomes is converted to a heterochromatic Barr body ==> Most genes of the Barr body are transcriptionally inactive ==> Conversion occurs during embryonic development in somatic cells of the body

Constitutive heterochromatin

Refers to chromosomal regions that are always heterochromatic and permanently inactive w/ regard to transcription => Usually contains highly repetitive DNA sequences, such as tandem repeats, rather than gene sequences

Sequence complexity

Refers to the # of times a particular base sequence appears throughout the genome of a species

Exons

Regions of an RNA molecule that remain after splicing has removed the introns

Centromeres

Regions that play a role in proper segregation of chromosomes during mitosis and meiosis => Most eukaryotic species have only one of them in their chromosomes => Function as a site for the formation of kinetochores, which assemble just before and during the very early stages of mitosis and meiosis

A, B, E

Select all these that are DNA sequences required for the replication and segregation of eukaryotic chromosomes (A) Telomeres at ends of chromosomes (B) Centromeres (C) Promoters at the starts of genes (D) Exons in the genes (E) Origins of replication (F) Introns in the genes

Origin of replication

Sequence of bacterial DNA that is a few hundred nucleotides in length and functions as an initiation site for assembly of several proteins required for DNA replication

Moderately repetitive sequences

Sequences found a few hundred to several thousand times in a genome • In a few cases, they are multiple copies of the same gene => Genes that encode rRNA are found in many copies => Histone protein-encoding genes are found in multiple copies b/c a large number of them are need for the structure of chromosomes • Some may play a role in regulation of gene transcription and translation • Some do not play a functional role and are derived from transposable elements (TEs)

Highly repetitive sequences

Sequences found tens of thousands or even millions of times throughout a genome => Each copy is relatively short, ranging from a few nucleotides to several hundred in length => The Alu family of sequences is a widely studied example that is found in humans and other primates ==> Each is a~300 bp long and derives its name from the observation that it contains a site for cleavage by a restriction enzyme known as AluI ==> This sequence represents about 10% of total human DNA and occurs ~every 4000-6000 bp ==> Evolutionary studies suggest that it arose 65 mya from a section of a single ancestral gene known as the 7SL RNA gene ===> Since that time, this gene has become a type of TE called a retroelement ==> Over the past 65 mya, the Alu sequence has been copied and inserted into the human genome many times and is now present in about 1,000,000 copies

Nucleoid associated proteins (NAPs)

Sets of DNA-binding proteins found in bacteria that facilitate chromosome compaction and organization • They either bend the DNA or act as bridges that cause different regions of DNA to bind to each other • Facilitate chromosome segregation and play role in gene regulation • Ex: histone-like nuceloid structuring (H-NS) proteins and structural maintenance of chromosomes (SMC) proteins

Repetitive sequences

Short DNA sequences that occur many times w/in a species' genome (A) A variety have been identified in many bacterial species (B) These sequences are found in multiple copies and are usually interspersed w/in the intergenic regions throughout the bacterial genome (C) They may play a role in a variety of genetic processes, including: (1) DNA folding (2) DNA replication (3) Gene regulation (4) Genetic recombination (D) Some are transposable elements that can move throughout the genome

Transposable elements (TEs)

Short segments of DNA that have the ability to move w/in a genome => Source of some moderately repetitive sequences that do not play a functional role

Matrix-attachment regions (MARs)

Sites in the chromosomal DNA that is anchored to the nuclear scaffold => Bind to specific proteins in the nuclear matrix, thus forming chromosomal loops => Also called scaffold-attachment regions (SARs)

Telomeres

Specialized regions of repeated sequences found at the ends of linear chromosomes that serve several important functions in the replication and stability of the chromosome => Prevent chromosomal rearrangements such as translocations => Prevent chromosome shortening in two ways (1) Protect chromosomes from digestion via enzymes called exonucleases that recognize the ends of DNA (2) An unusual form of DNA replication occurs at their ends to ensure that eukaryotic chromosomes do not become shortened w/ each round of DNA replication

Chromosomes

Structures w/in living cells containing genetic material

Chromatin

The DNA-protein complex found w/in eukaryotic chromosomes

Digestion

The Repeating Nucleosome Structure is Revealed by ______ of the Linker Region (1) Incubate the nuclei w/ low, medium and high concentrations of DNase. The conceptual level illustrates a low DNase I concentration (2) Isolate the DNA => This involves dissolving the nuclear membrane w/ detergent and treating the sample w/ the organic solvent phenol (3) Load the DNA into a well of an agarose gel and run the gel to separate the DNA pieces according to size => On the gel, also load DNA fragments of known molecular mass (marker lane) (4) Visualize the DNA fragments by staining the DNA w/ ethidium bromide, a dye that binds to DNA and is fluorescent when excited by UV light

Negatively

The chromosomal DNA in living bacteria is _________ supercoiled => In E. coil, about one supercoil occurs per 40 turns of double helix

Condensin

There are two proteins that drive the condensation (compaction) of interphase chromosomes into metaphase chromosomes. Those proteins are called _________ and cohesin

Cohesin

There are two proteins that drive the condensation (compaction) of interphase chromosomes into metaphase chromosomes. Those proteins are called condensin and ________

False

There is a close relationship b/w the complexity of a eukaryotic organism and genome size (T/F) ***Two closely related species of salamander have very different genome sizes despite similar complexities as organisms

D

W/ regard to the 30-nm fiber, a key difference b/w the solenoid and zigzag models is (A) the solenoid model suggests a helical structure (B) the zigzag model suggests a more irregular pattern of nucleosomes (C) the zigzag model doesn't include nucleosomes (D) both a and be are correct

• Eukaryotic chromosomes have centromeres and telomeres, which bacterial chromosomes lack • Eukaryotic chromosomes typically have many more repetitive sequences

What are some differences b/w the types of sequences found in eukaryotic chromosomes versus bacterial chromosomes?

Histones

What are the black arrows pointing at?

B

What are the components of a single nucleosome? (A) About 146 bp of DNA and histone proteins (B) About 146 bp of DNA and eight histone proteins (C) About 200 bp of DNA and 4 histone proteins (D) About 200 bp of DNA and 8 histone proteins

C, D, E

What are the defining features of eukaryotic chromosomes (Select all that apply) (A) Circular (B) Found in nucleoid (C) Found in nucleus) (D) Linear (E) Present in one or more sets (F) Only one copy ever present

C and E

What are the functions of telomeres? (A) Attachment of the chromosome to the mitotic spindle (B) Prevention of pairing of homologous chromosomes during mitosis (C) Prevention of chromosomal rearrangements (D) Prevention of recombination during mitosis (E) Prevention of chromosomal shortening

A, B, F, G

What are the key features of bacterial chromosome organization and structure? (A) Chromosomes are about a few million bp long (B) Chromosomes are generally circular (C) Chromosomes have centromeres and telomeres (D) Chromosomes are linear (E) Chromosomes are found in pairs (F) Chromosomes generally have thousands of different genes (G) Chromosomes have a single origin of replication (H) Chromosomes are tens of millions of bp long

(1) # of genes varies among different eukaryotes (2) Amount of repetitive sequences varies

What are the two reasons for the wide variation in genome sizes among eukaryotic species?

Protein attached to nuclear matrix filament

What is A?

Nuclear matrix filament

What is B?

Nuclear lamina

What is C?

Outer nuclear membrane

What is D?

Inner nuclear membrane

What is E?

Nuclear pore

What is F?

11 nm

What is the diameter of a nucleosome at its widest point?

The nuclear matrix helps to organize and compact the chromosomes w/in the cell nucleus and also aids in their condensation during cell division

What is the function of the nuclear matrix?

DNA

What is the pink arrow pointing at?

B

What kinds of filaments are used to construct the nuclear lamina? (A) Actin filaments (B) Intermediate filaments (C) Microtubules (D) Collagen fibers (E) Histones

Genome

What name is given to the entire complement of genetic material in an organism?

Sequences of genes

What types of sequences constitute mot of a bacterial genome?

A

Where is the nuclear lamina located? (A) Lining the inner nuclear membrane (B) B/w the inner and outer nuclear membranes (C) Inside the nuclear matrix (D) Lining the outer nuclear membrane

A, B. D

Which of the following are differences b/w bacterial and eukaryotic genomes? (A) The presence of genomes in organelles in eukaryotes (B) The number of chromosomes in the genome (C) The nature of the genetic material making up the genome (D) The structure of the chromosome(s) making up the genome

A

Which of the following is an example of a moderately repetitive sequence? (A) rRNA genes (B) Most protein-encoding genes (C) Both a and b (D) None of the above

Euchromatin

Would you expect to find active genes in regions of heterochromatin or euchromatin?