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HONR 1034 Chapter Notes - Chapter 12: Polytene Chromosome, Karyotype, Dna Supercoil

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ochretoad334
12 Jun 2018
School
GWU
Department
Honors
Course
HONR 1034
Professor
Patrnogic

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DNA Organization in Chromosomes
I. Viral chromosomes (not considered as a living entity because they need a hose to survive and transmit
themselves from one cell to another) → use a host to replicate themselves to transmit and pass on
A. Have a single nucleic acid molecule that is either DNA or RNA
B. Can be linear or circular and either single or double stranded
C. Based on the type of genome the virus carries, it determines the way it’s being replicated →
because they’re small and causing different types of diseases, they need to evolve quickly and
replicate quickly
D. Prokaryotic chromosomes are devoid of associated proteins and have less genetic information
II. Bacterial chromosomes (bacteriophage)
A. Single molecule (the usual case) of DNA that circular and double stranded
B. No nucleus because they are a prokaryote; the organelle doesn’t have its own membrane or define
structure, so the genetic material is localized in the nucleoid
C. Associated proteins
1. HU
2. H-NS → histone-like nucleoid structuring proteins → involved in the structuring of
forming the nucleoid and the process of regulating how genes will be expressed
III. Viruses, eukaryotes, and bacteria can all package long DNA molecules into a pretty small volume
IV. Supercoiling facilitates compaction of the DNA of viral and bacterial chromosomes
A. Characteristic of closed-circular molecules
B. Proposed during an experiment when polyoma DNA was seen to be subject to high speed
centrifugation
C. Closed-circular molecules are more compact and sediment more rapidly during centrifugation than
some linear molecules
D. Linear, double stranded DNA
E. Three distinct components → based on density and compactness of DNA
1. Three structures can be found in in DNA
2. Dense → circular and supercoiled
F. Linking number (L): number of complete turns
G. Experiment
1. Supercoiled DNA with E coli
2. Many domains
3. Negative supercoils → inserted along the axis
a) Spontaneous mechanisms for the structure
H. Advantages of circular DNA
1. The ends are connected so they don’t get damaged
2. Because two forks form, it can go faster and it supports what is dividing
V. Specialized chromosomes reveal variations in the organization of DNA
A. Two types of eukaryotic chromosomes: polytene and lampbrush
B. Polytene: found in various tissues in larvae of some flies and some plants
C. 200-600 micrometers long (big); demonstrate series of alternating bands and interbands
1. Individual bands sometimes called chromomeres (lateral condensations of material
along the axis of a chromosome
D. Can be seen in the nuclei of interphase cells
E. Large number of identical DNA molecules - polytene chromosomes represent paired homologs
1. Undergo replication, but without separation of strands or cytoplasmic division
2. Creates chromosomes that are parallel to one another
3. Each chromosome has its own pattern of bands which will be the same in each organism
4. Each band corresponds to a certain gene
5. Each time a band uncoils it’s called a puff, which is a bulge → manifestations of high
gene activity
6. For the gene to be active and readable it must be uncoiled
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Related Questions

1. In addition to identifying the genetic material, the experiments of Avery, MacLeod, and McCarty with different strains of Streptococcus pneumoniae demonstrated that
DNA is a double helix.
DNA may be taken up by bacterial cells and be active.
DNA is present in bacteriophage T2.
eukaryotic cells may be genetically transformed.
DNA binds to the cell wall of the bacterium.
2. In order to show that DNA in cell extracts is responsible for genetic transformation in Streptococcus pneumoniae, important corroborating evidence should indicate that _______ also destroy transforming activity.
temperatures high enough to kill cells
enzymes that hydrolyze proteins
enzymes that hydrolyze DNA
enzymes that hydrolyze polysaccharides
enzymes that hydrolyze RNA
3. Based on what you have learned about the experiments conducted by Griffith and Avery and colleagues with bacteria, which of the following would result in transformation of living R cells?
Pure RNA from S cells
Cell-membrane extracts from S cells
A mixture of pure RNA and protein from S cells
Cell-free extracts from S cells
Pure protein from S cells
4. A-T base pairs in a DNA double helix
form three hydrogen bonds with each other.
are more heat-stable than G-C base pairs.
are of a substantially different length than G-C base pairs.
are not accessible to DNA binding proteins.
are chemically distinct from G-C base pairs.
5. If 23 percent of the bases in a sample of double-stranded DNA are adenine, what percentage of the bases are uracil?
27
50
0
73
23
6. The uniform diameter of the DNA structure provides evidence for
antiparallel DNA strands.
a right-handed helix.
a double-stranded helix.
3′ end phosphorylation.
purine–pyrimidine pairing.
7. If a sequence of one strand of DNA is 5′-TGACTATC-3′, what is the complementary strand?
5′-ACTGATAG-3′
3′-TGACTATC-5′
3′-ACTGATAG-5′
3′-ACTGATAG-3′
5′-TGACTATC-3′
8. What structural aspect of the DNA facilitates dissociation of the two DNA strands for replication?
3′ end phosphorylation
Purine–pyrimidine pairing
Antiparallel DNA strands
Covalent bonds between sugars and phosphate groups
Hydrogen bonding between paired bases
9. If the Meselson–Stahl density gradient experiment had resulted in two bands of DNA molecules after only one round of replication, one containing only 15N and the second only 14N, this result would have indicated that replication was
unidirectional.
dispersive.
conservative.
bidirectional.

semiconservative.
10. The nucleoside analogue acyclovir, which is used to treat herpes simplex virus (HSV) infections, lacks a 3′ hydroxyl group (–OH). Predict what will happen if the host cell DNA polymerase incorporates a molecule of acyclovir into an elongating strand of HSV DNA.
The replication complex will no longer bind to origins of replication.
The DNA polymerase will only incorporate acyclovir molecules.
Acyclovir will bind single-strand binding proteins.
DNA polymerase will not be able to link a successive nucleotide.
Acyclovir will block the activity of the DNA helicase.
11. Which of the following does not demonstrate the stability of the DNA double helix?
Single-strand binding proteins are required to keep the strands apart.
Paired bases form hydrogen bonds.
High temperatures are required to denature it.
DNA synthesis requires energy.
DNA helicases require ATP.
12. What effect would a primase inhibitor have on DNA replication?
DNA polymerase would not be able to add bases to the DNA.
Primase would be blocked from joining the DNA replication complex.
Primase would not be able to provide primers for DNA polymerases.
DNA polymerase would not be able to use DNA as a template.
There would be no effect on DNA replication.
13. To replicate their DNA in a timely manner, most eukaryotic chromosomes
normally have uncoiled DNA.
have multiple origins of replication.
contain linear molecules of single-stranded DNA.
have two replication forks that move in the same direction.
are composed entirely of DNA.
14. Which statement about DNA replication is false?
Okazaki fragments are synthesized as parts of the leading strand.
Error rates for DNA replication are reduced by proofreading of the DNA polymerase.
The sliding clamp increases the rate of DNA synthesis.
Replication forks represent areas of active DNA synthesis on the chromosomes.
Ligases and polymerases function in the vicinity of replication forks.
15. In many eukaryotes, there are repetitive sequences called telomeres at the ends of chromosomes. After successive rounds of DNA replication, the _______ strand becomes shorter. In some cells, an enzyme called _______ repairs the shortened strand.
leading; telomerase
lagging; telomerase
lagging; DNA polymerase I
leading; DNA polymerase I
leading; replicase
16. A researcher studies normal human fibroblast cells. They can be maintained in culture but die off after about 30 cell generations. Unexpectedly, a colony of cells continues to survive and divide past 30 generations. Which scenario is most likely true for these cells?
DNA polymerase is constantly active.
Primase is able to extend the telomeres.
The mismatch repair system is extra efficient.
The telomerase gene is being expressed.
The cells do not need the ends of their chromosomes.
17. If DNA polymerase III introduces an incorrect nucleotide, what is the first corrective action made by the DNA repair system?
The replication complex excises the incorrect nucleotide.
The excision repair proteins remove the incorrect nucleotide.
The mismatch repair system scans for base-pairing mismatches.
There is no correction, because nucleotide errors by DNA polymerases are not repaired.
DNA ligase connects the correct nucleotide.
18. Choose the correct order of the following four events in the excision repair of DNA:
(1) Base-paired DNA is made complementary to the template.
(2) Damaged bases are recognized.
(3) DNA ligase seals the new strand to existing DNA.
(4) Part of a single strand is excised.
1, 2, 3, 4
2, 1, 3, 4
3, 4, 2, 1
2, 4, 1, 3
4, 2, 3, 1
19. Six complete cycles of PCR should result in a _______-fold increase in the amount of DNA.
64
32
12
128
6
20. When double-stranded DNA is heated to temperatures above 90°C, it denatures. Denaturation is a process that
breaks covalent bonds.
hydrolyzes DNA.
separates double-stranded DNA into two single strands.
causes new hydrogen bonds to form.
irreversibly destroys the double helical structure.

13. The arms of a human and the wing of a bat are _________________ structures, composed of the same bones that have been modified for different functions.

a. analogous
b. vestigial
c. homologous
d. convergent

14. Xeroderma pigmentosum is an autosomal recessive genetic disorder. People who are homozygous for the disease-causing allele have skin that is damaged by exposure to ultraviolet radiation; this can lead to skin cancer at an early age. The mutation that causes this disorder is in a gene that functions:

a. to repair DNA by excising (removing) nucleotides damaged by UV light.
b. in lysosomes, to break down lipids that otherwise accumulate in the nervous system.
c. to produce the UV blocking pigment melanin in the skin cells
d. in red blood cells to carry oxygen to the skin.

15. The Amish are a religious sect descended from a small group of colonists who came to the United States over 200 years ago. Their religious beliefs have kept them isolated from society. The Amish have a much higher than average incidence of both polydactyly (extra fingers and toes) and dwarfism in their communities. This is most likely explained by:

a. inheritance of acquired characters.
b. the founder effect.
c. disruptive selection.
d. natural selection.

16. In the structure of DNA that Watson and Crick proposed, the sides of the "ladder" of the DNA molecule are always the same distance apart, making the molecule a constant width. This occurs because when the bases hydrogen bond to form the rungs of the "ladder", a:

a. purine always pairs with a pyrimidine.
b. purine always pairs with a purine.
c. pyrimidine always pairs with a pyrmidine.
d. The structure of the double helix is not determined by how the bases pair.

17. The RNA transcript of DNA that travels to the cytoplasm, carrying the instructions to make a protein, is called:

a. rRNA.
b. tRNA.
c. mRNA.
d. RNA polymerase.

18. When DNA is replicated, the error rate is approximately one error for every 10,000 nucleotides copied. However, that error rate is reduced to only 1 error for every 1 billion nucleotides. The DNA sequence is "corrected" by:

a. repeating S phase to see if the error rate is lower the second time around.
b. enzymes that proofread the DNA and repair errors.
c. messenger RNA during the process of transcription.
d. Any errors made during DNA replication cannot be corrected. If errors are detected after S phase, the cell is destroyed.

19. Mendel's principle of segregation says that:

a. when gametes are formed, each gamete receives only one allele for a particular gene.
b. some genes are dominant to others.
c. a testcross must be used to determine the genotype of an organism with a dominant phenotype.
d. all of the above

20. Tay-Sachs disease is lethal before reproductive age, but the allele persists in Louisiana French Canadians because:

a. it is a dominant allele.
b. new mutations causing this disease are common in that population.
c. it is not expressed in the phenotype of heterozygous individuals.
d. the disease is contagious and can be transmitted by nonheritable means.

21. Physical features that are similar in organisms which are not closely related to each other are most likely a result of ____________. A good example of this is the similarities seen between some marsupial and placental mammals.

a. natural selection.
b. adaptation to similar environments
c. convergent evolution
d. All of the above phrases can be used to correctly fill this blank.

22. In humans, which of the following sex chromosome compliments could be found in males?

a. XY
b. XX
c. Y

23. The proteins that are associated with eukaryotic chromosomes:

a. help to package the DNA within the nucleus.
b. are involved in gene expression, through binding with the DNA.
c. may be replicating or transcribing the DNA.
d. All of these are true of proteins that are associated with eukaryotic chromosomes.

24. A sequence of DNA nucleotides that contains the information to produce a single protein is a(n):

a. codon.
b. gene.
c. polypeptide.
d. anticodon.
1. What recent research has indicated that studying Down Syndrome may hold a key to cancer growth and slowing tumor growth? In your answer be sure to mention the DSCR1 gene, angiogenesis suppression, and why individuals with Down’s Syndrome rarely have solid tumor growth. 2. Select your favorite chromosome and list the following: Three disorders that are found on this chromosome, Indicate the type of disorder (dominant, recessive) and the type of numerical or structural aberration. 3. Assume that crossing over does not occur in the region of each chromosome that is associated with the centromere. You have 46 centromeric regions in each cell, 23 that are copies of the DNA in your mother’s egg and 23 that are copies of the DNA father’s sperm. a. For any given gamete, what is the probability that all the centromeric regions will be copies of the same ones that you received from your mother? b. It has been estimated that the average person is heterozygous for at least 2,000 protein forming genes. How many different kinds of gametes is it theoretically possible for each person to produce? c. Considering the maternal and paternal origin of the centromeric regions alone, how many different kinds of gametes can you produce? 4. Find a current article on Telomerase (within the last year). Summarize the article and answer the following: What is telomerase? Why is it viewed as the fountain of youth? Attach the abstract or the first page. 5. Promiscuous Sun Flower has five lovers, but she has decided that the only true father of her child can have her hand in marriage. Sun’s Blood type is A- her five suitors blood types are as follows: a. Maury AB+ b. Elmer O+ c. Willie A- d. Jiggs B- e. Cousin it B+ 6. What is the epigenome. Explain why the study of the epigenome may not follow normal Mendelian genetics 7. Explain what is meant by the statement “Women are just as hemizygous as men”. 8. After having 10 children you remarry…… What is the probability of you now having a boy and then a girl, and then a girl, and then a boy, and then a boy or a girl, and then a girl? You now have 16 children…… 9. The genetic code has four codons for the amino acid Valine (GUG, GUC, GUU, GUA). Organisms have evolved to use some codes more than other codes. Which of the valine codes would you expect to be preferentially used in the genome of an algae growing in a hot spring at Yellowstone Park? EXPLAIN your answer 10. You discovered a new virus that needs to be studied. You begin by digesting the virus with protease (an enzyme that completely digests all proteins) until only amino acids remain. You then determine that the base composition of the viral nucleic acid is 38% Cytosine, 35% Glycine, 15% Thymine, and 12 % Adenine. To which class could this virus belong? EXPLAIN YOUR ANSWER a. Single-stranded RNA Virus b. Double-stranded RNA Virus c. Single-stranded DNA Virus d. Double=stranded DNA Virus e. None of the above because there is not enough information given to make a guess. 11. Adenine is found in numerous biological molecules (for example, DNA, RNA, NADH, ATP). You are now asked to explain the evolution of adenine and at least 5 of these biological (Adenine containing) molecules and how they may have evolved (the order).