Chapter 11 - Chromosome Structure & Organelle DNA Flashcards
Which statement is true regarding negative supercoiled DNA?
a. Negative supercoiled DNA is under-rotated and allows for easier strand separation during replication and transcription.
b. Negative supercoiled DNA is not usually seen in cells.
c. Negative supercoiled DNA has 10 base pairs per turn of its helix.
d. Negative supercoiled DNA carries more negative charges than does positive supercoiled DNA.
a. Negative supercoiled DNA is under-rotated and allows for easier strand separation during replication and transcription.
A circular DNA molecule 300 bp long has 20 complete rotations. This DNA molecule is:
A. positively supercoiled.
B. negatively supercoiled.
C. relaxed.
B. negatively supercoiled.
Which of the following statements regarding heterochromatin is false?
A. It is found at the centromeres and telomeres of all chromosomes
B. The inactive X-chromosome of female mammalian cells are made up of it
C. It is highly condensed during the cell cycle
D. It undergoes condensation and de-condensation during the cell cycle
E. Both answers B and D are correct
D. It undergoes condensation and de-condensation during the cell cycle
If a piece of chromatin contained 200 copies of the histone H4, then how many nucleosomes would be present?
100
How does bacterial DNA differ from eukaryotic DNA?
Bacterial DNA is not complexed with histone proteins and is circular.
Neutralizing their positive charges would have which effect on the histone proteins?
a. They would bind the DNA tighter.
b. They would bind less tightly to the DNA.
c. They would no longer be attracted to each other.
d. They would cause supercoiling of the DNA.
b. They would bind less tightly to the DNA.
How many copies of the H2B histone would be found in chromatin containing 50 nucleosomes?
100
Which of the following is a characteristic of DNA sequences at the telomeres?
a. One strand consists of guanine and adenine (or thymine) nucleotides.
b. They consist of repeated sequences.
c. One strand protrudes beyond the other, creating some single-stranded DNA at
the end.
d. All of the above
d. All of the above
Most of the genes that encode proteins are found in:
a. unique-sequence DNA.
b. moderately repetitive DNA.
c. highly repetitive DNA.
d. All of the above
a. unique-sequence DNA.
What evidence supports the endosymbiotic theory? (three main points)
- Many modern protists are hosts to endosymbiotic bacteria. 2. Mitochondria and chloroplasts have ribosomes that are similar in size and shape to bacterial ribosomes (which is why antibiotics affect mitochondria). 3. Gene sequences in mtDNA and cpDNA are most similar to DNA sequences in eubacteria.
In a few organisms, traits encoded by mtDNA can be inherited from either parent. This observation suggests that in these organisms,
a. mitochondria do not exhibit replicative segregation.
b. heteroplasmy is present.
c. both sperm and eggs contribute mitochondria to the zygote.
d. there are multiple copies of mtDNA in each cell.
c. both sperm and eggs contribute mitochondria to the zygote.
In its organization, chloroplast DNA is most similar to
a. bacteria.
b. archaea.
c. nuclear DNA of plants.
d. nuclear DNA of primitive eukaryotes.
a. bacteria.
The tertiary structure of DNA is its?
Chromosome structure
What causes supercoiling?
over- or under-wound / twisting upon itself to relieve the torsional stress.
What is the most relaxed/stable confirmation of DNA, and how many bp does it contain per turn? What real-life example does it look like?
B-form DNA is the most relaxed at about 10 bp/turn.
It looks like a phone cord.
Positive supercoiling = __-rotated & in the __ direction as the helix (to the __); Negative = __-rotated and in the __ direction of the helix (__). Most cellular DNA is __ supercoiled because it facilitates transcription (easier to ‘__’ and read).
over-rotated; same; (right);
under-rotated; opposite; (left).
negatively; ‘open’
T or F: Supercoiling leads to a break in phosphodiester bonds - this is how transcription is started.
False
T or F: positive supercoiling enables better compaction of DNA.
False - both positive and negative lead to the same compactness.
What is the formula for calculating the number of rotations one should have in order to determine positive/negative supercoiling or B-form?
# of bp / 10 = relaxed DNA (this is what B-form would be) If >, it is positively supercoiled; if < it is negatively supercoiled.
What happens to supercoiled DNA if a phosphodiester bond (backbone) is broken? What is the molecule that can do this, and how does it do it?
Torsional stress is relieved by the helix rotating around the central axis and will spontaneously go towards a fully relaxed state.
Topoisomerases can add or remove supercoils by cleaving one of the phosphodiester bonds, rotating the ends around each other and rejoining the broken ends.
Linear dsDNA can’t have supercoiling unless…?
One end is constrained/controlled.
When do topoisomerases come to the rescue?
When the replication bubble is advancing and the supercoiling becomes to great (too much torsional stress).
Type I topoisomerase cleaves how many strands? Which subcategory is found in prokaryotic cells, and what kind of supercoil does it address (neg or pos)? For Eukaryotic organisms?
Type I cleaves one strand.
Topo1A is found in prokaryotes and only relaxes neg strands.
Topo1B is found in eukaryotes and relaxes neg AND adds positive supercoils.
Which topoisomerase breaks both strands? Does it add or remove rotations?
Type II.
It can add or remove depending on the specific enzyme - they are more varied and complex than type I.
Prokaryotic DNA is associated with a ___ amount of protein as compared to eukaryotes. Their DNA is ____ within the cell and anchored by ____ into what’s called a _____ (the suffix meaning “like”).
limited.
clumped; protein; nucleoid
In eukaryotic organisms, interphase chromatin is less condensed than ___ chromatin, but it is still highly ____ and very _____.
metaphase; condensed; structured
Euchromatin is ___ active. It undergoes ____ and ____ throughout the cell cycle, contains most of the ___ DNA that is used for synthesis of ___.
transcriptionally
condensation; decondensation; transcribed; RNA
Heterochromatin remains highly ____ during the cell cycle and has little to no ____. It stains ___ in karyotyping. It is found at ___ and ___ of all chromosomes, as well as other sites. The ___ female mammalian X-chromosome is almost all heterochromatin.
condensed; transcription.
darkly.
centromeres; telomeres.
inactive
“Histones are highly conserved from an evolutionary standpoint” - what does this mean?
Most organisms have almost identical histones, so it has been conserved through the evolution of many species… “if it ain’t broke, don’t fix it”.
Histones are ____ charged, and have a high percentage of the amino acids ____ and ____. The 5 major are __, __, __, __, and __. They account for approximately __% of the protein in chromatin.
positively; arginine; lysine.
H1, H2A, H2B, H3, H4; 50%
Chromatin proteins other than histones are called ___ proteins. They’re a __ collection that make up the other __% of chromatin protein.
nonhistone
heterogeneous; 50%
Isolated chromatin resembles beads on a string; these beads are ___. If you add a small amount of DNAse, the string portion is ___ due to a break in the ___ bonds, and you’re left with beads containing approx ___ bp. The addition of more DNAse leaves you with a ___ that has approx ___ bp; and adding a bit more leaves you with the ___ containing approx __ bp.
nucleosomes
nicked; phosphodiester; 200 bp.
chromatosome; 167 bp; nucleosome; 147 bp
The progressive addition of DNAse to degrade DNA not associated with histones is called? What do these experiments reveal about chromatin?
Nuclease Protection Assay
Chromatin has a fundamental repetitive structure.
The chromatosome has approx ___ bp - 145-147 bp on the ___; and approx 20 bp associated with ___. Each chromatosome is connected by approx ___ to ___ bp of linker DNA.
167 bp; nucleosome; H1.
30 - 40 bp
Nucleosomes coil to form a 30 nm fiber called a ___. Each loop of the coil is about 20 Kbp - 100 Kbp long. These loops are the basic structure of ___ chromatin.
solenoid.
Interphase
From G2 through to M phase, chromatin condenses and forms ___ nm-long loops that condense and fold into to ___nm-wide fibers that are further coiled into ___ nm-long loops seen in ____.
300nm long; 250nm wide; 700nm long; metaphase
Polytene chromosomes are the result of ___ - DNA keeps dividing but the cell never does. It leads to about __ copies of DNA per chromosome. Polytene chromosomes are unique in that they are ___ and produce detailed ___ when stained.
endoreduplication.
500
align; bands
If polytene chromosomes are exposed to thermal stress, they form ___ ___. The phenomenon of this response is called a __ __ __. The response is ___ from prokaryotes to humans. The genes responsible are called ___ ___ ___ that make proteins called molecular ____: they bind to cellular proteins to help prevent denaturing. The puffing is really ___ of chromatin for RNA ___.
chromosomal puffs
Heat shock response.
Universal.
Heat shock genes; chaperones.
relaxation; transcription
Polytene chromosomes are unusual in that they are ___ during ___.
synapsed; interphase
___ ___ is somewhat comparable to nuclear protection assay. But in this assay, DNA associated with active __ __ (i.e. transcription) is more sensitive to degradation.
DNAse sensitivity.
gene expression
In the DNAse sensitivity experiment using chick erythroblasts; globin genes showed ___ sensitivity during the first 24 hours. During the first 5 days, ___ globin genes showed sensitivity, but ___ globin genes did not. After about 14 days, ___ globin genes showed sensitivity, but ___ globin genes did not.
no.
embryonic; adult
adult; embryonic
Methylation as well as variations of both __ and __ proteins within chromatin cause ____ changes. Some of these changes are ___ and can be ____ to progeny.
histone; nonhistone; epigenetic.
stable; passed
The first centromeres studied at the molecular level were isolated from ___. They’re centromeres are extremely ___ and can only be viewed using an ___ ___. Other eukaryotic organisms have centromeres that are typically ___ of copies of ___ ___ ___ that span more than ___ Kbp.
yeast
small; electron microscope
thousands; short tandem repeats; 100 Kbp
Telomeres are structured with ___ repeats of ___ DNA sequences expressed by 5’ Cn (__ or __)m - 3’.
tandem; short; A or T
In humans, telomeres are sequences of CCCTAA repeated anywhere from ___ to ___ times. The length of the repeat is ___ varying from cell to cell. The Cs are always oriented toward the __ end of the chromosome.
250 - 1500.
dynamic
3’
The first artificial chromosomes were hybrids built form __ and __ and were called __ __ __ (or YACs). More recently, BACs (__ __ __) and MACs (__ __ __) have been constructed.
Each artificial chromosome has 3 parts: __, a pair of __, and an __ of ___.
Yeast; protozoans; yeast artificial chromosomes
bacterial artificial chromosomes; mammalian artificial chromosom
centromere; telomeres; origin of replication.
YACs, BACs, and MACs enabled __ of large stretches of DNA which was critical in the ___ ____ project.
cloning; human genome project.
The amount of DNA per haploid cell called the __-___. Drosophila has 35x more than ___ ____, but only twice the number of genes; additionally, humans have 10x more than Drosophila, but only __x as many genes. These differences are called the __-___ ___.
C-value.
E. coli; 2x; C-value paradox
Tm is __ __, and it’s the temp at which the dsDNA becomes __% ssDNA. When the molecule is heated, the __ break and the strands separate. It’s also called __.
thermal melting; 50; H-bonds; denaturation
DNA with a higher __+__ will have a higher ___ due to the presence of __ H-bonds.
When DNA is slowly cooled, it will ___ (aka ___); the complimentary sequences will reform.
G+C; Tm; 3
Renature; reanneal
DNA hybridization involves ___ complementary strands of DNA from ___ organisms and was technology at the heart of ___ DNA. The bases don’t have to be a perfect ___, just reasonably ____.
annealing; different; recombinant.
match; complimentary
Renaturation experiments revealed that eukaryotes have 3 classes of DNA sequences: ___ ___ DNA; ___ ___ DNA, and ___ ___ DNA.
Unique sequence; moderately repetitive, and highly repetitive.
Unique sequence was inferred using ___ / ___ experiments: repeated sequences would ___ faster than unique sequences.
denaturation/renaturation.
anneal
Some unique sequence DNA codes for ___, and others have functions that are still ___. Approx __% to __% of genes in this category are present as a single copy with the remaining as part of ___ ___.
proteins; unknown.
25% to 50%; gene families
Gene ___ arose by duplication followed by ___ ___. An example are the ___ genes. Humans have seven different _-___ genes grouped around chromosome ___ that code for ___ molecules. Another subcategory of this family are the ___, of which there are several hundred members.
families; evolutionary divergence.
Globulin
β-globulin; 11; hemoglobin
immunoglobulins
____ repetitive DNA consists of sequences from 150 - 300bp repeated ___ of times; the majority of these sequences are genes that code for ___.
Moderately repetitive; thousands; tRNA
Some moderately repeated DNA is ___ repeated (self-explanatory); others are ___. The ___ DNA are scattered ___ the genome; they may encode regulatory ___.
An example of ___ DNA are the ___ sequences; these are approx 200bp and repeated at least __M times thought the human genome.
tandemly; interspersed.
interspersed; throughout; RNAs
interspersed; Alu; 1M
Two sub categories of interspersed, moderately repetitive DNA are ___ ___ ___ and ___ ___ ___ (SINEs and LINEs). __ are examples of SINEs; whereas ____ are examples of LINEs (the latter are no longer active in ___; just old evolutionary relics at this point).
Short INterspersed Elements; Long INterspersed Elements.
Alu; transposons; humans
Highly repetitive DNA are sequences approx 10bp long repeated about __M times or more. They cluster around ___ and ____ and are rarely transcribed. There function seems to be for ____ rather than transcription which makes sense given their location.
1M
Centromeres and telomeres.
stabilization
The Encode Project showed that “___ DNA” (coined by Francis Crick) appears to be expressed as more than 4 million ___ RNAs, and their function is in ____ gene ____ (and therefore the amount of ___ produced).
“junk DNA”; micro RNAs; regulating gene expression; protein
The ___ of functional genes varies widely among chromosomes. For example, human chromosome 19 has approx 26 genes per Mbp; whereas the ___ arms of chromosome 13 has approx 3 genes per MBP, but the __ arms have approx 30 genes per Mbp!!
density
long
short
mtDNA and cpDNA encode ____, ___ and some ___ used by the organelles; but most of the genes that encode product needed by the organelles are encoded in the ___.
polypeptides; rRNA (ribosomal); tRNA (transfer); nucleus
mtDNA and cpDNA are genetically similar to ____; this is the main justification for the ___ theory.
Their genetic similarity to ____ explains why some antibiotics have serious side effects.
eubacteria; endosymbiotic theory
eubacteria
At 100Kbp, F factor is about 5x larger than human ___.
Human __ encodes 2 rRNAs, 22 tRNAs, and 13 proteins whereas yeast __ is __x larger but encodes 2 rRNAs, 25 tRNAs, and 16 proteins making it about the same as humans.
mtDNA
mtDNA; 5x; mtDNA
Vertebrate mtDNA mutates ~__ - __x faster than the nuclear genome, but the number of genes and organization remain relatively ___. In fact, most copies of mtDNA are ____.
In contrast, plant cpDNA mutates ~ __x as fast as the nuclear genome.
5 - 10x faster; constant.
identical
1/10 (or only 10% of the rate of)
Damage to mtDNA is associated with aging likely due to ___ from ___ ____.
oxidation; oxidative phosphorylation
The majority of proteins needed by organelles are encoded in the ____; and the sequences of these genes bear strong resemblance to ____ genes. This suggest that DNA from the original ___ relocated to the nucleus; this is termed ___ DNA.
nucleus; eubacterial
endosymbiont; promiscuous
