fill in the blanks in the following brief description of the
experiment with Streptococcus pneumoniae that identified which biological molecule carries heritable genetic information.
Cell-free extracts from S strain cells of S. pneumoniae were fractionate
purify
R strain
pathogenic
S strain
DNA
transform
R strain
pathogenic
(or S strain)
In a DNA double helix
(d) the two DNA strands run antiparallel.
On the diagram of a small portion of a DNA molecule in Figure Q5-3, match the labels
below to the numbered label lines.
1- 5' end
2- phosphate
3- sugar
4- 3' end
5- hydrogen bond
6- base
The structures of the four bases in DNA are given in Figure Q5-4.
A. Which are purines and which are pyrimidines?
B. Which bases pair with each other in double-stranded DNA?
A. Adenine and guanine are purines; cytosine and thymine are pyrimidines
B. Cytosine pairs with guanine and adenine with thymine
A ribbon model of the DNA double helix showing the major and minor grooves is reproduced in Figure Q5-6.
Figure Q5-6
A. Draw on the figure to indicate the length of a single full helical turn.
B. How many base pairs per turn does a DNA helix have?
B. There are ~10 base pairs per turn when the DNA has the standard conformation
Given the sequence of one strand of a DNA helix:
5?-GCATTCGTGGGTAG-3?
give the sequence of the complementary strand and label the 5? and 3? ends.
5' -CTACCCACGAATGC- 3'
Which of the following sequences can fully base-pair with itself?
A. 5?-AAGCCGAA-3?
B. 5?-AAGCCGTT-3?
C. 5?-AAGCGCAA-3?
D. 5?-AAGCGCTT-3?
E. 5?-AATTGGCC-3?
(D.)
5' -AAGCGCTT -3'
3' -TTCGCGAA -5'
-This double stranded DNA molecule has the same sequence whether read forward or backward, which is defined as palindromic.
The DNA from two different species can often be distinguished by a difference in the
(a) ratio of A + T to G + C.
When double-stranded DNA is heated, the two strands separate into single strands in a process called melting or denaturation. The temperature at which half of the duplex
DNA molecules are intact and half have melted is defined as the Tm.
Do you think Tm i
Tm depends on the identity and concentration of other molecules in the solution. High salt concentrations are more effective at shielding the two negatively
charged phosphate-sugar backbones in the double helix from each other, so the two strands repel ea
When double-stranded DNA is heated, the two strands separate into single strands in a process called melting or denaturation. The temperature at which half of the duplex
DNA molecules are intact and half have melted is defined as the Tm.
Under standard co
The Tm increases as the proportion of G + C bases increases and as the length increases. The thermal energy required for melting depends on how many hydrogen bonds between the strands must be broken. Each G-C base pair contributes three hydrogen bonds, wh
When double-stranded DNA is heated, the two strands separate into single strands in a process called melting or denaturation. The temperature at which half of the duplex
DNA molecules are intact and half have melted is defined as the Tm.
Calculate the pre
Inserting values into the equation in part (B) gives Tm = 59.9 + (0.41 � 50) -(675/100) = 73.65�C, which is about twice the normal temperature of the human body and nearly too hot to touch.
You and a friend want to split a double-stranded DNA molecule so you each have half. Is it better to cut the length of DNA in half so each person has a shorter
length, or to separate the strands and each take one strand? Explain.
It is better to separate the stands and each take a single strand, because all of the information found in the original molecule is preserved in a full-length single strand but not in a half-length double-stranded molecule.
In the original 1953 publication describing the discovery of the structure of DNA, Watson and Crick wrote, "It has not escaped our notice that the specific pairings we have postulated immediately suggest a possible copying mechanism for the genetic materi
Watson and Crick meant that the complementary base pairing of the strands allows a single strand to contain all of the information necessary to direct the synthesis of a new complementary strand.
In principle what would be the minimum number of consecutive nucleotides necessary to correspond to a single amino acid to produce a workable genetic code? Assume that each amino acid is encoded by the same number of nucleotides. Explain your reasoning.
As there are 20 amino acids used in proteins, each amino acid would have to be encoded by a minimum of three nucleotides. For example, a code of two consecutive nucleotides could specify a maximum of 16 (42) different amino acids, excluding stop and start
On average how often would the nucleotide sequence CGATTG occur in a DNA strand 4000 bases long? Explain your reasoning.
As 46 (= 4096) different sequences of six nucleotides can occur in DNA, any given sequence of six nucleotides would occur on average once in a DNA strand 4000 bases long.
In eucaryotic __________________, DNA is complexed with proteins to form __________________.
chromosomes
chromatin
The paternal and maternal copies of human
Chromosome 1 are __________________, whereas the paternal copy of Chromosome 1 and the maternal copy of Chromosome 3 are __________________.
homologous
nonhomologous
Cytogeneticists can determine large-scale
chromosomal abnormalities by looking at a patient's __________________.
karyotype
Fluorescent molecules can be used to paint a chromosome by virtue of DNA __________________, and thereby to identify each chromosome using microscopy.
hybridization
Define a gene.
A gene is a segment of DNA that stores the information required to specify the particular sequence found in a protein (or in some cases, the sequence of a structural or catalytic RNA)
Consider two different species of yeast that have similar genome size. Is it likely that they contain a similar number of genes? A similar number of chromosomes?
A similar genome size indicates relatively little about the number of genes and virtually nothing about the number of chromosomes. For example, the commonly
studied yeasts Saccharomyces cerevisiae (Sc) and Schizosaccharomyces pombe (Sp) are separated by r
Figure 5-15 in the textbook shows the G + C content and genes found along a single chromosome. Is there any relationship between the G + C content and the
locations of genes?
Regions of the chromosome with a high density of genes tend to have about 50% G + C, whereas those with few genes tend to have a lower G + C content. This is
generally true in most organisms.
How many centromeres are in each cell? What is the main function of the centromere?
46
-46 per cell, one on each chromosome. centromeres play a key role in the distribution of chromosomes to daughter cells during mitosis
How many telomeres per cell? What is their main function?
92
-92 per cell, 2 on each chromosome. Telomeres serve to protect the ends of chromosomes and to enable complete replication of the DNA of each chromosome all the way to its tips.
How many replication origins per cell? What is their main function?
>200
-probably around 10,000 replication origins in a human cell. The DNA sequences direct the initiation of DNA synthesis needed to replicate chromosomes.
Each chromosome is a single molecule of __________________ whose extraordinarily long length can be compacted by as much as __________________-fold during __________________ and tenfold
more during __________________. This is accomplished by binding to
__
DNA
1000-fold
interphase
mitosis
proteins
nuclear envelope
The structure of the DNA-protein complex, called __________________, is highly __________________ over time.
chromatin
dynamic
Nucleosomes are present in [procaryotic/eucaryotic] chromosomes, but not in
[procaryotic/eucaryotic] chromosomes.
eucaryotic
procaryotic
A nucleosome contains two molecules each of histones [H1 and H2A/H2A and H2B] as well as histones H3 and H4.
H2A and H2B
A nucleosome core particle contains a core of histone with DNA wrapped around it approximately [twice/three times/four times].
~twice
Nucleosomes are aided in their formation by the high proportion of [acidic/basic/polar] amino acids in histone proteins.
basic
Nucleosome formation compacts the DNA into approximately [one-third/onehundredth/one-thousandth]
of its original length.
one-third
Interphase chromosomes contain both darkly staining
__________________ and more lightly staining __________________.
heterochromatin
euchromatin
Genes that are being transcribed are thought to be packaged in a __________________ condensed type of euchromatin.
less
Nucleosome core particles are separated from each other by stretches of __________________ DNA.
linker
A string of nucleosomes coils up with the
help of __________________ to form the more compact structure of the __________________.
Histone H1
30 nm fiber
The __________________ model describes the
structure of the 30 nm fiber.
zigzag
The 30 nm chromatin fiber is further compacted by the formation of __________________ that emanate from a central __________________.
loops
axis
In which of the following instances can the state of chromatin packing differ? Explain your reasoning.
A. Between different cells of the same organism.
B. In different stages of the cell cycle.
C. In different parts of the same chromosome.
D. In different
All answers are correct.
-Chromatin differs most dramatically during the different stages of the cell cycle. (B)
Evidence suggests that the replication of DNA packaged into heterochromatin occurs later than the replication of other chromosomal DNA. What is the simplest possible
explanation for this phenomenon?
The DNA double helix in heterochromatin may be so tightly packed and condensed that it is inaccessible to the proteins that bind replication origins, including the DNA replication machinery. It may take extra time to remodel the chromatin to make it more
If the mottled coloring of calico cats is due to X-chromosome inactivation, which of the following statements will be TRUE?
(a) Calico cats can be male or female.
(b) Female calico cats will be the same color as their mother.
(c) The mottled color is due
(d) Calico cats with identical patterns will be rare.
-Since the pattern of X-chromosome inactivation is established randomly over several days of embryonic development, at a stage where the embryo has quite a few cells, it is unlikely that 2 cats will in
Chromatin remodeling complexes act to regulate gene expression and other DNA processes that involve access to DNA. A characteristic component of chromatin
remodeling complexes is a powerful ATPase. Why is ATPase activity needed?
For DNA to be accessible�for transcription or some other process�noncovalent bonds must be broken in order to change interactions between DNA and its packaging proteins. This energetically unfavorable feat can be accomplished by harnessing the energy rele
Imagine that you have developed a method to isolate all of the histones bound to a single human chromosome. You then examine histones from the inactive X chromosome in an individual female and compare them to histones from her active X chromosome. Do you
Based on the information presented in Chapter 5, it seems reasonable to propose that the nucleosomes on the heterochromatic inactive X chromosome might contain histone H3 tails with distinctive modifications. Indeed, in line with the histone code hypothes
Figure Q5-23
The lowest spot (as observed in lanes 2, 4, and 5) has a length of about 150 nucleotides. Can you propose what it is and how it arose?
The lowest spot represents DNA of a length similar to that of the segment of DNA found in a nucleosome core particle. Partial digestion with an enzyme like
M-nuclease causes breaks in the DNA backbone primarily within the linker DNA or other DNA segments
Figure Q5-23
The lanes are as follows:
1. "marker" containing known DNA fragments of indicated lengths.
2. grew cells in glucose, visualized DNA near Sweetie gene.
3. grew cells in galactose, visualized DNA near Sweetie gene.
4. grew cells in glucose, vis
The ladder of bands with longer lengths probably corresponds to stretches of DNA associated with increasing numbers of nucleosomes (1, 2, 3, 4, 5, and so
on). In support of this proposal, adjacent bands differ in size by roughly 200 nucleotides, which is
Figure Q5-23
Notice the faint spots and extensive smearing in lane 3, suggesting the DNA could be cut almost anywhere near the Sweetie gene after growth of the cells in galactose. This was not observed in the other lanes. What probably happened to the DNA
Based on the ability of M-nuclease to cut anywhere near Sweetie after growth in galactose, it appears that the DNA is no longer protected from digestion by binding to histones. Perhaps the wrapping of DNA within the nucleosomes has been loosened considera
Figure Q5-23
What kinds of enzymes might have been involved in changing the chromatin structure from lane 2 into lane 3?
The main candidates for enzymes that catalyzed the nucleosome alterations near Sweetie are chromatin remodeling complexes and enzymes that covalently
modify histone tails with methyl, acetyl, or phosphate groups.
Figure Q5-23
Do you think that gene expression of Sweetie is higher, lower, or the same in galactose compared to glucose? What about Salty?
As the chromatin appears to have been loosened near Sweetie, it seems likely that Sweetie gene expression is increased when cells are grown in galactose rather
than glucose, whereas Salty gene expression is likely to be the same under the two conditions.