Chapter 11 - Chromosome Structure & Organelle DNA

Question 1

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.

Answer 1

a. Negative supercoiled DNA is under-rotated and allows for easier strand separation during replication and transcription.

Question 2

A circular DNA molecule 300 bp long has 20 complete rotations. This DNA molecule is:
A. positively supercoiled.
B. negatively supercoiled.
C. relaxed.

Answer 2

B. negatively supercoiled.

Question 3

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

Answer 3

D. It undergoes condensation and de-condensation during the cell cycle

Question 4

If a piece of chromatin contained 200 copies of the histone H4, then how many nucleosomes would be present?

Answer 4

100

Question 5

How does bacterial DNA differ from eukaryotic DNA?

Answer 5

Bacterial DNA is not complexed with histone proteins and is circular.

Question 6

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.

Answer 6

b. They would bind less tightly to the DNA.

Question 7

How many copies of the H2B histone would be found in chromatin containing 50 nucleosomes?

Answer 7

100

Question 8

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

Answer 8

d. All of the above

Question 9

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

Answer 9

a. unique-sequence DNA.

Question 10

What evidence supports the endosymbiotic theory? (three main points)

Answer 10

1. 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.

Question 11

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.

Answer 11

c. both sperm and eggs contribute mitochondria to the zygote.

Question 12

In its organization, chloroplast DNA is most similar to

a. bacteria.
b. archaea.
c. nuclear DNA of plants.
d. nuclear DNA of primitive eukaryotes.

Answer 12

a. bacteria.

Question 13

The tertiary structure of DNA is its?

Answer 13

Chromosome structure

Question 14

What causes supercoiling?

Answer 14

over- or under-wound / twisting upon itself to relieve the torsional stress.

Question 15

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?

Answer 15

B-form DNA is the most relaxed at about 10 bp/turn.

It looks like a phone cord.

Question 16

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).

Answer 16

over-rotated; same; (right);
under-rotated; opposite; (left).

negatively; ‘open’

Question 17

T or F: Supercoiling leads to a break in phosphodiester bonds - this is how transcription is started.

Answer 17

False

Question 18

T or F: positive supercoiling enables better compaction of DNA.

Answer 18

False - both positive and negative lead to the same compactness.

Question 19

What is the formula for calculating the number of rotations one should have in order to determine positive/negative supercoiling or B-form?

Answer 19

# of bp / 10 = relaxed DNA (this is what B-form would be)
If >, it is positively supercoiled; if < it is negatively supercoiled.

Question 20

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?

Answer 20

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.

Question 21

Linear dsDNA can’t have supercoiling unless…?

Answer 21

One end is constrained/controlled.

Question 22

When do topoisomerases come to the rescue?

Answer 22

When the replication bubble is advancing and the supercoiling becomes to great (too much torsional stress).

Question 23

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?

Answer 23

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.

Question 24

Which topoisomerase breaks both strands? Does it add or remove rotations?

Answer 24

Type II.

It can add or remove depending on the specific enzyme - they are more varied and complex than type I.

Question 25

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”).

Answer 25

limited.

clumped; protein; nucleoid

Question 26

In eukaryotic organisms, interphase chromatin is less condensed than ___ chromatin, but it is still highly ____ and very _____.

Answer 26

metaphase; condensed; structured

Question 27

Euchromatin is ___ active. It undergoes ____ and ____ throughout the cell cycle, contains most of the ___ DNA that is used for synthesis of ___.

Answer 27

transcriptionally

condensation; decondensation; transcribed; RNA

Question 28

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.

Answer 28

condensed; transcription.

darkly.

centromeres; telomeres.

inactive

Question 29

“Histones are highly conserved from an evolutionary standpoint” - what does this mean?

Answer 29

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”.

Question 30

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.

Answer 30

positively; arginine; lysine.

H1, H2A, H2B, H3, H4; 50%

Question 31

Chromatin proteins other than histones are called ___ proteins. They’re a __ collection that make up the other __% of chromatin protein.

Answer 31

nonhistone

heterogeneous; 50%

Question 32

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.

Answer 32

nucleosomes

nicked; phosphodiester; 200 bp.

chromatosome; 167 bp; nucleosome; 147 bp

Question 33

The progressive addition of DNAse to degrade DNA not associated with histones is called? What do these experiments reveal about chromatin?

Answer 33

Nuclease Protection Assay

Chromatin has a fundamental repetitive structure.

Question 34

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.

Answer 34

167 bp; nucleosome; H1.

30 - 40 bp

Question 35

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.

Answer 35

solenoid.

Interphase

Question 36

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 ____.

Answer 36

300nm long; 250nm wide; 700nm long; metaphase

Question 37

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.

Answer 37

endoreduplication.

500

align; bands

Question 38

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 ___.

Answer 38

chromosomal puffs

Heat shock response.

Universal.

Heat shock genes; chaperones.

relaxation; transcription

Question 39

Polytene chromosomes are unusual in that they are ___ during ___.

Answer 39

synapsed; interphase

Question 40

___ ___ is somewhat comparable to nuclear protection assay. But in this assay, DNA associated with active __ __ (i.e. transcription) is more sensitive to degradation.

Answer 40

DNAse sensitivity.

gene expression

Question 41

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.

Answer 41

no.

embryonic; adult

adult; embryonic

Question 42

Methylation as well as variations of both __ and __ proteins within chromatin cause ____ changes. Some of these changes are ___ and can be ____ to progeny.

Answer 42

histone; nonhistone; epigenetic.

stable; passed

Question 43

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.

Answer 43

yeast

small; electron microscope

thousands; short tandem repeats; 100 Kbp

Question 44

Telomeres are structured with ___ repeats of ___ DNA sequences expressed by 5’ Cn (__ or __)m - 3’.

Answer 44

tandem; short; A or T

Question 45

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.

Answer 45

250 - 1500.

dynamic

3’

Question 46

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 ___.

Answer 46

Yeast; protozoans; yeast artificial chromosomes

bacterial artificial chromosomes; mammalian artificial chromosom

centromere; telomeres; origin of replication.

Question 47

YACs, BACs, and MACs enabled __ of large stretches of DNA which was critical in the ___ ____ project.

Answer 47

cloning; human genome project.

Question 48

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 __-___ ___.

Answer 48

C-value.

E. coli; 2x; C-value paradox

Question 49

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 __.

Answer 49

thermal melting; 50; H-bonds; denaturation

Question 50

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.

Answer 50

G+C; Tm; 3

Renature; reanneal

Question 51

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 ____.

Answer 51

annealing; different; recombinant.

match; complimentary

Question 52

Renaturation experiments revealed that eukaryotes have 3 classes of DNA sequences: ___ ___ DNA; ___ ___ DNA, and ___ ___ DNA.

Answer 52

Unique sequence; moderately repetitive, and highly repetitive.

Question 53

Unique sequence was inferred using ___ / ___ experiments: repeated sequences would ___ faster than unique sequences.

Answer 53

denaturation/renaturation.

anneal

Question 54

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 ___ ___.

Answer 54

proteins; unknown.

25% to 50%; gene families

Question 55

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.

Answer 55

families; evolutionary divergence.

Globulin

β-globulin; 11; hemoglobin

immunoglobulins

Question 56

____ repetitive DNA consists of sequences from 150 - 300bp repeated ___ of times; the majority of these sequences are genes that code for ___.

Answer 56

Moderately repetitive; thousands; tRNA

Question 57

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.

Answer 57

tandemly; interspersed.

interspersed; throughout; RNAs

interspersed; Alu; 1M

Question 58

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).

Answer 58

Short INterspersed Elements; Long INterspersed Elements.

Alu; transposons; humans

Question 59

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.

Answer 59

1M

Centromeres and telomeres.

stabilization

Question 60

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).

Answer 60

“junk DNA”; micro RNAs; regulating gene expression; protein

Question 61

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!!

Answer 61

density

long

short

Question 62

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 ___.

Answer 62

polypeptides; rRNA (ribosomal); tRNA (transfer); nucleus

Question 63

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.

Answer 63

eubacteria; endosymbiotic theory

eubacteria

Question 64

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.

Answer 64

mtDNA

mtDNA; 5x; mtDNA

Question 65

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.

Answer 65

5 - 10x faster; constant.

identical

1/10 (or only 10% of the rate of)

Question 66

Damage to mtDNA is associated with aging likely due to ___ from ___ ____.

Answer 66

oxidation; oxidative phosphorylation

Question 67

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.

Answer 67

nucleus; eubacterial

endosymbiont; promiscuous