how is the nucleus divided? what divides them?
its divided into subcompartments, its divided by functions and there are no membranes
if there are no membranes in a nucleus, is it structured?
yes
name 4 advantages to the organization of the nucleus?
compartmentalization, specilization, regulation, and protection
what does heterochromatin do?
lines the innter membrane of the nucleus
what are nuclear pores?
gaps in the heterochromatin and the nuclear membrane, through which everything is transported
when is DNA called chromatin?
when its with a protein
what does a nucleolus do?
as the largest organelle in the nucleus it is responsible for rRNA, rProteins and ribosomal subunits
what needs to happen in order to get mRNA out of the nucleus?
it needs to turn into rRNA
what does the fibrillar center do?
it makes rDNA
what does the dense fibrillar center do?
it processes rRNA
what does the granular center do?
it packages rRNA and rProteins
what is FISH?
fluorescent in situ hybridization: creates markers for specific chromosomes
what do non-ionic detergents and salts do?
the detergent disrupts the membrane, and the salts remove histones
what do you do if you want to "fix" the contents of the nucleus in place?
you associate it with other proteins
what does lamin do in nuclear matrix? (2)
1. forms channels for RNA/DNA/proteins are formed and then shipped out 2. provide structure in the nuclear matrix (and help in mRNA processing)
what are lamin filaments comprised of?
protofilaments woven together
what do centrioles do?
form microtubules
what needs to happen to the nucleus inorder for the cell to divide? how does this happen?
the nucleus has to be broken down, phosphorylation
what are the 5 phases of cell division (inorder)
mitosis, prophase, metaphase, anaphase, telophase
what are laminopathies? name 4 examples
diseases with laminins in the nucleus. progeria(huntingtons syndrome), muscular dystrophy, cardiomyopathy, lipodystrophy
how can the nuclear pore regulate movement?
it can orient proteins toward or away from the nucleus
how do you isolate the proteins of the nuclear pore complex?
you isolate them by electrophoresis
what is the isoelectric point?
the pH at which proteins have no charge
pyruvate kinase is directed ___ the nucleus, as a response to _____
toward, lysine rich environment
nucleoli (plural of nucleus :) ) is a ____ structure
dynamic
what are karyopherins?
ferry transporters", that transport things in/out of the nucleus
which way do importins transport? exportins?
in, out
to get GDP to GTP you need ______
RAN-GAP
to get GTP to GDP you need ______
RAN-GEF
what is the role of RAN-GTP?
to unload the "cargo" from the importin
what does a heterokaryon allow you to do?
fuse together two different DNA
the concentration of RAN-GEF is ____ in cytoplasm than in the nucleus, conversely the RAN-GAP concentration is _____ in the cytoplasm than in the nucleus. so what does this do?
higher, lower. creates a concentration gradient that drives transport
does the nuclear pore complex require ATP to function? then what kind of transport does it do?
no, passive transport
what are 4 things that proteins do?
protect, repair, regulate use (help identify genes), package
what kind of chromosomes do eukaryotes have?
linear
what kind of chromosomes do bacteria have
circular
what is used inorder to condense chromosomes?
super coils
what is the most energetically favorable position for chromosomes? what will happen if it deviates from this?
where you have 10.4 basepairs per turn. it will turn to get back to this lowest energy state.
in a supercoil, a right turn is ____ and a left turn is ____
negative, positive
what are what are topoisomerases?
negative supercoils through coupling to ATP hydrolysis
in a DNA supercoil, what is the chain wrapped around? how does it stay around this?
solenoid in association with a histone core, its alittle bit "underwound
aside from the increased "surface area", in a super coil, what is an added bonus to having a histone core?
it is really stable
what are 3 characteristics of constituitive heterochormatin?
1. always condensed 2. methylated 3. highly repetative
what does epigentic mean?
that its not the sequence of proteins that is important, its the variety of proteins that is
on a haploid chromosome, there are knobs (the little part) and centromeres (the big part), where is the info kept?
mostly in the centromeres but sometimes the knobs can act like centromeres
what happens if there are 2 centromeres on a haploid chromosome (that is, a knob that is acting like a centromere and a centromere)?
whoever is bigger wins
what is a point centromere?
where the centromere has one attachment to the centromere
what is a regional centromere?
where there are a few attachment sites on the centromere
what is a holocentric chromosome?
where the whole thing is a centromere
what is the primary centromeric repeating unit called?
the alpha satellite
what does a cen-pa centromere do?
act like a beacon for all other centromeres
what keeps chromatids together?
cohesins
what happens if your chromosomes don't have a telomere? what does this mean?
they will be sticky, they will clump up and not be able to replicate
in RNA replication, which strand will be shorter (parent, or daughter)? why?
daughter because the RNA gets cut back out
what does a T-loop do? what is it?
protects the ends of the chromosome, and maintains chromosome integrity (prevents stickyness). its the single stranded portion of the 3' (daughter) terminus gets tucked inside the double stranded DNA molecule
what is the C-value paradox?
the size of the genome has nothing to do with the complexity of the organism, but it has to do with the number of genes.
what is the biggest factor in protein denaturation? what are 3 other factors?
ionic strength. size, % ratio of g-c bonds to a-t bonds, and complexity of the protein
of the base pair bonds (g-c, a-t) which require the most energy to break? why?
g-c, it has 3 hydrogen bonds where as a-t has 2 hydrogen bonds
how does Na+ concentration impact DNA
as [Na+] increases it weakens the pulling power of the phosphate groups, which make the hydrogen bonds between base pairs stronger.
what did Watson and Cricke do?
they proposed the model of DNA
if you "grab" the DNA with your right hand, and your thumb is facing up, what is the orientation?
right
if you "grab" the DNA with your left hand and your thumb is facing up, what is the orientation
left
what are the 3 forms of DNA? describe
B DNA (right handed), A DNA (right handed, compressed), and Z DNA (left handed and occurs when there are alot of repeatative bases.)
what characteristics does replication have? (3)
semiconservative, bidirectional, and regulated
what did Meselson and Staht do?
the came up with the idea of a isopycnotic gradient (where you can separate isotopes out of solution by centrifuging for days)
what needs to happen in order to differentiate between dispersive and semiconservative replication?
you need to carry it out a second generation (p1-->f1-->f2)
replication is _____. how does that work?
bidirectional. it has a bubble that grows on both ends.
how does the nucleus sort it cellular organelles?
they are sorted by function --> no membranes
what are 4 advantages to how the nucleus is structured?
compartmentalization, specialization, regulation, protection
what is the nuclear envelope?
a double membrane that divides the nucleus from the cytoplasm
what is the nuclear lamina?
meshwork that lines the nuclear envelope
what is the nuclear matrix?
insoluble protein network that criscosses through nuclear space
what is the nuclear pore complex?
gaps in the heterochromatin and the nuclear membrane
what is chromatin?
stuff that composes the chromosomes (DNA is always with proteins, so we call it chromatin)
what are "speckles"?
mRNA processors are limited to 30-50 sites called speckles
what is the nuclear skeleton? what does it do?
a network of fibrous proteins, that forms channels for "shipping" RNA, DNA, and proteins
what does the nuclear matrix do?
it acts as a workbench for transcription: chromatin loops are anchored to nuclear matrix
what does the nuclear lamina do?
it provides structure in nuclear matrix, and it helps in processing stuff
in bacteria, what kind of proteins generate loops?
non-histone
if you were to remove a histone from the condensed DNA what would it (the histone) look like?
it would look like a scaffold where DNA can attach by looping.
____ is/are an example of a dynamic nuclear subcompartment, the assembly of which is dependent upon _____
the nucleolus: the cells requirement for protein synthesis
newly synthesized mRNA molecules that have been labeled with radioactively or fluorescently labeled precursors would be associated with the ____.
fibrils of the nuclear matrix
nuclear lamina disassembly prior to mitosis is though to be induced by ____ by a _____
phosphorylation of lamins, cyclin-dependent protein kinase
which of the traits below is characteristic of the classical nuclear localization signals?
twisted peptide backbones
_____ that line the cnetral channel of the nuclear pore complex possess ____ and have been called "flexible gates" because of their role in nuclear import and export.
nucleoporins; phenylalanine-glycines repeats
after transport into the nuclear compartment, what meets the importin-cargo complex and what effect does it have on the complex?
Ran-GTP, causes the importin-cargo complex to dissassemble
The ran-GTP gradient across the nuclear envelope is maintained by....
energy released by GTP hydrolysis or GTP/GDP gradient
what is the evidence that histone amino acid sequences are heavily conserved?
the H4 histone of peas and cows vary in only 2 amino acids out of 102
if chromatin is treated with nonspecific nucleases ____, a direct consequence of ____.
200 bp fragments are generated; association of DNA with nucleosomes
what ____ have/has been removed from chromatin prior to being prepared for electron microscopy it is possible to see ____
H1 histones; the 10 nm fiber
____ bonds form between the ____ of DNA and the ____ amino acid residues of the histones
ionic bonds; phosphate groups; positively-charged
what is the packing ratio of DNA in nucleosomes? of DNA in the 30 nm fibers of chromatin
7:1; 40:1
hat happens if histone H1 is selectively extracted from compacted chromatin (20 nm fibers)?
30 nm fibers uncoil to form a thinner, more extended beads on a string filament
chromatin that is specifically inactivated during certain phases of an organism's life or in certain types of differentiated cells is called ____.
facultative heterochromatin
histone tail modifications may influence chromatin structure and function because _____ (2)
modified residues serve as docking sites for non-histone proteins, and modified residues alter associations between histone tails
why is freshly made strands of DNA shorter than its complement?
its RNA primer is removed and replaced with DNA
what does telomerase do?
it lengthens the 5' end to fill the gap
what is it surprising that centromeric DNA sequences are so variable even between related species?
centromere function is essential
how do histones associated with centromeric DNA differ from other histones in the nucleus?
centromeric DNA contains a H3 histone variant CENP-A
in herited characteristics that are not strictly dependent on or encoded in DNA sequences are said to be examples of _____
epigenetic inheritance
type of replication results in the integrity of both parental strands being disrupted?
dispersive replication
bacteria are grown in medium contain ammonium chloride for many gernations, so that all DNA is made of fully "heavy" DNA. bacteria are moved to this medium (so now this DNA will be "light"). what would the DNA look like after 2 generations?
75% are made of light strand, and 25 percent are the heavy strand.
cultured mammalian cells grown in thymidine for many generations were allowed to undergo replication in the presence of bromodeoxyuridine (which replaces thymidine in DNA) after 2 rounds of replication, what does the DNA look like?
half of the chromatids have 2 strands that conain bromodeoxyuridine, and half of the chromatids have 1 strand lacking bromo and 1 strand containing it.
Replication begins at ____ and is said to be_____ from this point
the origin; bidirectional
The replication fork generates _______ supercoils in the _______ portion of the DNA molecule.
positive, unreplicated
Why is an intact, linear double helix an ineffective template for DNA polymerase?
It has a 3'-hydroxyl group, but lacks a template.
DNA polymerases add nucleotides in a ____ direction and move along a template in a ____ direction.
5'�>3', 3'�>5'
The DNA strand growing toward the replication fork grows ______ in a 5'�>3' direction as the replication fork advances and has historically been called the ________.
continuously, leading strand
The _______ strand fragment grows away from the replication fork toward the ___- end of the previously synthesized fragment to which it is subsequently linked.
discontinuous, 5'
When Okazaki incubated bacteria in [3H]-thymidine for ______ and immediately killed them, the radiolabel was found as part of ________; if the cells were incubated in labeled DNA precursor for _____, most of the incorporated radioactivity became part of _
a few seconds, small DNA fragments, 1 to 2 minutes, a large DNA molecule
what is an additional advantage for using RNA primers during intiation of a strand in replication?
Errors are more likely to occur during initiation so a removable RNA segment provides opportunity for correction
How can the replication of both DNA strands by two tethered polymerases be accomplished when the template strands run in opposite directions?
The DNA of the lagging strand loops back on itself so it has same orientation as the leading strand template.
_____ is a noncatalytic component of the DNA polymerase III holoenzyme that keeps the polymerase associated with the DNA template and therefore provides _____.
clamp; processivity
what evidence suggests that the sequence of DNA was unimportant in the timing of replication?
The inactive, heterochromatized X chromosome in female mammals replicates late in S phase, while the active euchromatic X chromosome replicates at an earlier stage.
What evidence suggests that the assembly of DNA into nucleosomes is a very rapid event?
Electron micrographs of replicating DNA show nucleosomes forming on both daughter duplexes very near the replication fork.
The backbone of a DNA strand is ____; the covalent bonds that compose a strand of DNA are ____.
made up of alternating phosphate and sugar groups; 3'-5'-phosphodiester linkages
You isolate DNA from a particular organism and analyze it. The amount of adenine was 6 �moles and the A+T/G+C ratio is 4.0. How much guanine should be in the sample?
1.5 �moles
What statement below explains the uniform width of the DNA molecule along its entire width?
A pyrimidine nitrogenous base always pairs with a purine nitrogenous base.
The building blocks of a nucleotide are ___________.
a pentose sugar, a phosphate group and a nitrogenous base
DNA binding proteins often can read the sequence of nucleotides along the DNA without having to separate the chains. How do they do this?
The DNA binding proteins often contain domains that fit into the DNA grooves.
DNA that is relaxed and in its most energetically favorable conformation _________.
has ~10 base pairs per turn of DNA
DNA in a cell is typically ____ and will therefore become ____ to maintain a stable conformation
underwound; negatively supercoiled
You are studying two strands of DNA. They have exactly the same length, but the first one has a very high G + C/A + T ratio of 3.4. The second DNA strand has a more moderate G + C/A + T ratio of 2.3. Which of the two strands will have the highest melting
the first strand because it contains more H bonds
A genome is equivalent to the genetic information that is present in a ______ set of chromosomes.
haploid
How is the extent of DNA denaturation usually measured?
Absorbance of UV light by DNA increases as DNA denatures.
The base composition of DNA that is required to "open" for its function should be:
AT-rich, the smaller number of H bonds in that region of the gene will allow strand separation
____ is not a factor that determines the rate of renaturation of a given DNA preparation?
the source of the DNA
DNA sequence present in at least 10,000 copies per genome, that reanneals very rapidly and is typically present in clusters.
highly repetitive DNA
In reannealing experiments with denatured eukaryotic DNA, nonrepeated DNA sequences _______.
are very slow to hybridize
What is one explanation for the wide discrepancies in genome sizes from species to species?
Genomes have an extremely variable number of DNA sequences that do not code for proteins.
What percentage of the human genome codes for the amino acids in our proteins?
about 1.5%
The building blocks of a nucleotide are ___________.
a pentose sugar, a phosphate group and a nitrogenous base
According to Watson and Crick's proposal, each new DNA double helix _______.
contains one strand from the original DNA molecule and one newly synthesized strand
DNA sequence typified by short sequences of DNA (five to a few hundred base pairs in length) repeated a large number of times in tandem.
satellite DNAs
Satellite DNAs have been localized to what location during in situ hybridization studies?
centromere
Noncoding, moderately repeated DNA sequences are _________.
scattered throughout the genome as individual elements
what is the principle of hybridization?
if you have DNA you can renature and denature it
where would be a good site to start DNA replication?
an aread that is A-T rich
in bacteria, how fast is replication?
1000 nucleotides per second
in eukaryotes, how fast is replication?
100-200 nucleotides per second
which DNA is more complex: bacteria or eukaryotes?
eukaryotes
how does DNA replication regulated in eukaryotes?
by PO4 cyclin-dependent kinases
what happens when RNA opens up?
the RNA primer/polymerase "primes" the way to replication
why does eukaryotic DNA take longer to replicate?
because it has to move the nucleosomes
what acts like velcro to help importins through the nuclear pore complex?
phenylalanine-glycine repeats
what must be present for the kinetichore to form?
CEN-PA variant
what are the 2 jobs of RAN-GTP in nucleus
1. unload imported cargo 2. loads exported cargo to exportation
what happens when GTP is non-hydrolyzable?
it makes it worthless