Chromosomes
the structures within cells that contain the genetic material.
Genome
refers to a complete set of genetic material in a particular cellular compartment.
Difference between prok and Euk for genome
Bacteria usually has a single circular chromosome while eukaryotes, the genome, refers to the complete set of chromosomes that resides in the cell nucleus. Euk. have a mitochondrial genome while plants also have a chloroplast genome.
primary function of genetic material
to store the information needed to produce the characteristics of an organism,
chromosomal sequences facilitate 4 important processes
the synthesis of RNA and cellular proteins, the replication of chromosomes, the proper segregation of chromosomes, and the compaction of chromosomes so they can fit within living cells.
Viruses
small infectious particles that contain nucleic acid as their genetic material, surrounded by a protein coat, or capsid.
bacteriophages
viruses that infect bacteria. They may also contain a sheath, base plate, and tall fibers.
What do viruses not contain
energy producing enzymes, ribosomes, and or cellular organisms.
host cells
the cells viruses infect for making new viruses
structure of viruses
nucleic acid molecules ( RNA and DNA), surrounded by a capsid, or protein coat. Other viruses will also contain an envelope composed of a membrane and spike proteins.
viral genome
the genetic material that a virus contains. the genome can be DNA or RNA but never both, and it can either be single or double stranded DNA, and it can be linear or circular.
directed assembly
when virus assembly requires the participation of noncapsid proteins. These proteins direct the proper assembly of the virus.
functions of noncapsid proteins
Some proteins, called scaffolding proteins catalyze the assembly process and are transiently associated with the capsid. When the virus is done being assembled the scaffolding proteins are expelled form the mature virus. There are also proteins that act a
nucleoid
this is where a bacterial cell's chromosomes are found. The DNA in a nucleoid is in direct contact with the cytoplasm of the cell.
Bacterial chromosome
most are circular however some are linear. Has a few million base pairs and has a few thousand genes.
Structural genes
nucleotide sequences that encode proteins, and account for the majority of bacterial DNA.
Intergenic regions
the non transcribed regions of DNA located between adjacent genes.
origin of replication
a sequence that is a few hundred nucleotides in length. Bacterial chromosomes only have one of these. These nucleotide sequence functions as an initiation sire for the assembly of several proteins required for DNA replication.
repetitive sequences
These have been identified in many bacterial species. These sequences are found in multiple copies and are usually interspersed within the intergenic regions throughout the bacterial chromosome. Some of these sequences are transposable elements which move
What does the formation of chromosomal loops help make do?
helps make the bacterial chromosome more compact.
loop domains
is a segment of chromosomal DNA folded into a structure that resembles a loop. DNA binding proteins anchor the base of the loops in place. and loop domains help aid compaction of bacterial chromosomes.
DNA supercoiling
the two strands within DNA already coil around each other and the formation of additional coils are due to twisting forces.
How do twisting forces affect DNa structure
A left handed twist ( underwinding) can either produce fewer turns or a negative supercoil. While a right handed twist ( overwinding) produces more turns or a positive supercoil. When a DNa structure has more or less than 10 bp per turn it is unstable.
topoisomers
DNA conformations that differ with regard to supercoiling.
What is chromosome function influenced by
DNa supercoiling
Negative supercoiling consequences
Makes chromosomes more compact and therefore helps to decrease the size of the bacterial chromosome, creates tension in DNA strand that may be released by DNA strand separation. DNA strand separation enhances genetic activities such as replication and tra
How does bacterial DNA become negatively supercoiled
DNA gyrase, also known as topoisomerase 2, which contains four subunits ( two A and two B), introduces negative supercoils ( or relaxes positive supercoils) using energy from ATP. To alter supercoiling DNa gyrase has two sets of jaws that allow it to grab
Besides for adding negative supercoils what else can DNA gyrase do
DNA gyrase in bacteria and topisomerase 2 in eukaryotes can untangle DNA molecules.
topoisomerase 1
can relax negative supercoils
what does negative supercoiling promote?
strand separation
overview of DNA gyrase
DNA gyrase is composed of A and B subunits. The DNa binds to the lower jaws ( the A subuitys( and then the DNA wraps around the A subunits in a right handed direction. The upper jaws clamp onto DNA. Tehn the DNA held in the lower jaws is cut and the DNa i
which two things inhibit gyrase
quinolones and coumarins however they do not inhibit eukarytoic topoisomerase.
Eukaryotic chromosomes
Eukarytoic species has one or more sets of chromosomes and each set is composed of several different linear chromosomes. Usually contains many more genes than bacteria does. The chromosomes are located within a separate cellular compartment known as nucle
chromatin
DNA-protein complex found within eukaryotic chromosomes. it can change its shape and composition during the life of a cell.
how do we explain the difference in genome size?
Accumulation of repetitive DNA sequences present in many copies.
What three types of regions are required for chromosomal replication and segregation
origins of replication, centromeres, and telomeres.
Centromeres
regions that play a role in the proper segregation of chromosomes during mitosis and meiosis. They function as a site for the formation of kinetochores.
kinetochore
composed of a group of cellular proteins that link the centromere to the spindle apparatus during mitosis and meiosis ensuring the proper segregation of the chromosomes to each daughter cell.
telomeres
these are found at the end of linear chromosomes. Telomeres prevent chromosomal rearrangements such as translocations. They also prevent chromosome shortening in two ways.
How do telomeres prevent chromosome shortening
Telomeres protect chromosomes from digestion via enzyme called exonucleases that recognize the ends of DNA. Second and unusual form of DNa replication may occur at the telomere to ensure that eukaryotic chromosomes do not become shortened with each round
Where are genes located on chromosomes
between the centromeric and telomeric regions along the entire eukaryotic chromosome.
introns
noncoding intervening sequences. They make structural genes longer.
what is in DNA sequences and then the percentage of each one.
repetitive DNA> introns and other parts of genes such as enhancers> unique noncoding DNa >regions of genes that encode proteins ( exons).
sequence complexity
refers to the number of times a particular base sequence appears throughout the genome.
moderately repetitive sequence
are found a few hundred to several thousand times in the genome. They may playa role in the regulation of gene transcription and translation. Ex. genes that encode rRNA, histone genes.
transposable elements
segments of DNA that have the ability to move within the genome.
Highly repetitive sequences
found tens of thousands or millions of times in the genome. Each copy of this sequence is relatively short. Ex. Alu family--> restriction enzyme.
retroelement
seen in the Alu gene and its function is that it can be transcribed into RNA copied into DNA and inserted into the genome.
tandem array
Seen in moderately and highly repetitive sequences. It is a very short nucleotide sequence and is repeated many times ina row. They can be long and are seen in centromeric regions.
what is the significance of highly repetitive sequences
they may be important in the proper segregation of chromosomes during meiosis 1.
the rate of renaturation of complementary DNa strands provides what
A way to to distinguish between unique, moderately repetitive, and highly repetitive sequences.
Rate of renaturation for moderately/highly repetitive sequences and unique DNA.
FAST-highly repetitive sequences
Intermediate- moderately repetitive sequences
SLOW- unique DNA.
second order equation
-dC/dt=kC^2. The rate depends on the concentration of both reactants -C1 and C2. Its rate is proportional to the product of the concentrations of both strands.
-dc
a change in concentration of a single strand.
dt
with respect to time
k
constant rate
C^2
which is also equal to -C1 times C2 but since -c1 is equal to C2 it is C^2.
equation for determining the concentration of the single stranded DNA changes from time zero to a later time.
C/C0=1/1+ k2C0t.
C
concentration of a single stranded DNa at a later time, t
C0
the concentration of single stranded DNA at time zero.
k2
the second order rate constant for renaturation
Explain results of the equation
Ex. If you get .4 from the equation it means that after a certain period of time, 40 percent of DNA is still in the single stranded formation and 60 percent has renatured into the double stranded form.
nucleosome
the repeating structural unit within eukaryotic chromatin. a double stranded segment of DNA wrapped around an octamer of histone proteins. Each octamer contains eight histone subunits, two copies each of four different histone proteins.
histone proteins
consists of globular domain and a flexible charged amino terminus called an amino terminal tail. They have a large number of positively charged lysine and arginine amino acids.
Arginines
They play a huge role in binding to the DNA. Arginines within the histone proteins form electrostatic and hydrogen bonding interactions with the phosphate groups along the DNA backbone.
What are the four different histone proteins
H2A, H2B, H3, and H4.
H1
Called the linker histone. it binds to the DNa in the linker region between nucleosomes and may help to compact adjacent nucleosomes. Less tightly bound to DNA than the core histones.
Hypothesis for the nucleosome structure experiment created by Markus Noll
Dnase 1 should preferentially cut the DNA in the linker region thereby producing DNA pieces that are about 200 bp in length.
REsults form Nolls experiment
at high DNase 1 concentrations the entire sample of chromosomal DNA was digested into fragments of approx. 200 bp in length. this result is predicted by the beads on string model.
why did some fragments come out to 400 or 600 bp
if one linker region was not cut, a Dna piece would contain two nucleosomes and be 400 bp in length. If two consecutive linker regions were not cut a DNA piece would contain three nucleosomes containing 600 bp.
30 nm fiber
nucleosomes associate with each other for a form a more compact structure, 30 nm in diameter.
when H1 is not bound when treated with moderate salt concentrations.
beads on a string, but not as compact when there is H1 histones.
H1 histones bound to linker region and therefore..
nucleosomes are more compact.
What is the third level of compaction
It involves interactions between the 30 nm fibers and a filamentous network of proteins in the nucleus called the nuclear matrix.
Nuclear matrix
consists of two parts, the nuclear lamina: a collection of fibers that line the inner nuclear membrane. These fibers are composed of intermediate filament proteins. And the internal nuclear matrix, which is connected to the nuclear lamina and fills the in
Function of the proteins of the nuclear matrix
Involved in compacting the DNA into radial loop domains, similar to those described for the bacterial chromosome.
matrix attachment regions ( MARs)/ scaffold attachment regions ( SARs)
interspersed at regular intervals throughout the genome. The MARs bind to specific proteins in the nuclear matrix thus forming chromosomal loops.
why is the attachment of radial loops to the nuclear matrix important?
In addition to compaction the nuclear matrix serves to organize the chromosomes within the nucleus.
chromosome territory
Each chromosome in the cell nucleus is located in a discrete chromosome territory. These territories can be viewed when interphase cells are exposed to mutliple florescent molecules that recognize specific sequences on particular chromosomes.
heterochromatin
tightly compacted regions of chromosomes. Usually transcriptionally inactive. In heterochromatin radial loops become even more condensed. It is most abundant in the centromeric regions of the chromosomes and to a lesser extent in the telomeric regions.
euchromatin
less condensed regions and reflect areas that are capable of gene transcription. the 30 nm fibers forms radial loops domains here.
constitutive heterochromatin
chromosomal regions that are always heterochromatic and permanently inactive with regard to transcription. Usually contains highly repetitive DNA sequences such as tandem repeats rather than gene sequences.
Facultative heterochromatin
refers to chromatin that can occasionally interconvert between heterochromatin and euchromatin. Ex. when in females one of the two X chromosomes is converted into a heterochromatic Barr body.
What promotes the formation of metaphase chromosomes
condensin and cohesin
During interphase chromosomal DNA is found in which compaction most commonly
euchromatin, in which the 30 nm fibers form radial loop domains that are attached to a protein scaffold.
In which phase are chromosomes entirely heterochromatic
by the end of prophase, sister chromatids are entirely heterochromatic.
scaffold
is formed from nonhistone proteins of the nuclear matrix.
In highly condensed chromosomes such as though found in metaphase the radial loops are highly compacted and remain anchored to...
scaffold
a high concentration of salt will..
remove both the linker and core histones and the high compaction of chromosomes is lost.
Steps in the chromosomal compaction in eukaryotics.
DNA double helix, wrapping of DNA around a histone octamer, ( nucleosomes, beads on a string), formation of a three dimensional zigzag pattern via histone H1 and other DNA binding proteins which creates a 30 nm fiber, and then anchoring of radial loops to
What are the two multiprotein complexes in cells
codensin and cohesin
what do condensin and cohesin do
they playa critical role in chromosomal condensation and sister chromatid alignment respectively. Therefore cohesin is released during prophase when you want the arms to separate
SMC proteins
proteins that stand for structural maintenance of chromosomes. These proteins use energy from ATP to catalyze changes in chromosome structure. These proteins actively fold, tether, and manipulate DNA strands. They are dimers that have a V shaped structure
structure of SMC proteins
It is a dimer that consists of a hinge, arm, and head regions. The head regions bind and hydrolyze ATP. Codensin and cohesin have additional protein subunits not shown here. N indicates the amino terminus C indicates the carboxyl terminus.
cohesin
after s phase cohesin complexed bind along each chromatid thereby facilitating their attachment to each other. During the middle of prophase cohesin is released from the chromosome arms but some cohesin remains in the centromeric regions. At anaphase the
bacterial chromosomes
most but not all contain circular chromosome DNA, a typical chromosome is a few million bp in length, most bacterial species contain a single type of chromosome but it may be present in multiple copies, several thousand different genes are interspersed th
eukaryotic chromosomes 2
Usually linear, a typical chromosome is 10s of millions to hundreds of millions of base pairs, occur in sets since many species are diploid which means that somatic cells contain 2 sets of chromosomes, genes are interspersed throughout the chromosome and
difference between point and regional centromeres
point: a defined DNA sequence that is about 125 bp in length.
regional: centromeres found in more complex eukaryotes that are much larger and contain many copies of tandemly repeated DNA sequences.
Distinctive feature of centromeres in eukaryotics
the histone H3 is replaced with CENP-A
What kind of sequences do eukaryotes contain
unique, moderately repetitive, and highly repetitive.
unique/nonrepetitive sequences
these are found once or a few times within the genome. Ex. structural genes.
beads on a string model
the nucleosomes are said to be attached by linker regions and resemble a beads on a string and this shortens the length of the DNA molecule about sevenfold.
non histone proteins
these also bind to the linker region and play a role in the organization and compaction of chromosomes and their presense may affect the expression of nearby genes.
Explain on the conceptual level the DNase 1 experiment
before digestion the nucleosomes look like beads on a string, after digestion DNA is cut in the linker region, then DNA in aqueous phase
Explain on the experimental level the Dnase 1 experiment
incubate the nuclei with low, medium, and high concentrations of DNase 1, extract the DNA and this involves dissolcing the nuclear membrane with detergent and extracting with the organic solvent phenol, load the DNA int a well of agarose gel and run the g
interpreting the data
at high DNase 1 concentrations we see that the entire chromosomal DNA was digested into fagements of 200 bp. While at low concentrations there were 400 and 600 bp because it did not always cut. these results support the beads on string model.
The two models suggested for the 30 nm fiber
the solenoid and zigzag model.
solenoid model
suggests a helical structure in which contact between the nucleosomes produces a symmetrically compact structure within the 30 nm fiber.
zigzag structure
Based on techniques such as cryoelectron microscopy. and the linker regions within the 30 nm structure are variably bent and twisted and little face to face contact occurs between nucleosomes.
Markus Null
the nucleosome and linker regions experiment.