Chapter 5 Bio 002
For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. In eucaryotic __________________, DNA is complexed with proteins to form __________________. 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 __________________. Cytogeneticists can determine large-scale chromosomal abnormalities by looking at a patient's __________________. Fluorescent molecules can be used to paint a chromosome by a technique that employs DNA __________________, and thereby to identify each chromosome by microscopy. bands chromatin chromosomes condensation kinetochore homologous extended non homologous hybridization karyotype
In eukaryotic *chromosomes*, DNA is complexed with proteins to form *chromatin*. The paternal and maternal copies of human Chromosome 1 are *homologous*, whereas the paternal copy of Chromosome 1 and the maternal copy of Chromosome 3 are *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 a technique that employs DNA *hybridization*, and thereby to identify each chromosome by microscopy.
For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. Interphase chromosomes contain both darkly staining __________________ and more lightly staining __________________. Genes that are being transcribed are thought to be packaged in a __________________ condensed type of euchromatin. Nucleosome core particles are separated from each other by stretches of __________________ DNA. A string of nucleosomes coils up with the help of __________________ to form the more compact structure of the __________________. A __________________ model describes the structure of the 30 nm fiber. The 30 nm chromatin fiber is further compacted by the formation of __________________ that emanate from a central __________________. 30 nm fiber active chromatin axis beads-on-a-string euchromatin heterochromatin histone H1 histone H3 histone H4 less linker loops more synaptic complex zigzag
Interphase chromosomes contain both darkly staining *heterochromatin* and more lightly staining *euchromatin*. Genes that are being transcribed are thought to be packaged in a *less* condensed type of euchromatin. Nucleosome core particles are separated from each other by stretches of *linker* DNA. A string of nucleosomes coils up with the help of *histone H1* to form the more compact structure of the *30 nm fiber*. A *zigzag* model describes the structure of the 30 nm fiber. The 30 nm chromatin fiber is further compacted by the formation of *loops* that emanate from a central *axis*.
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 accessible to the proteins required to initiate and perform DNA replication.
Because hydrogen bonds hold the two strands of a DNA molecule together, the strands can be separated without breaking any covalent bonds. Every unique DNA molecule "melts" at a different temperature. In this context, Tm, melting temperature, is the point at which two strands separate, or become denatured. Order the DNA sequences listed below according to relative melting temperatures (from lowest Tm to highest Tm). Assume that they all begin as stable double- stranded DNA molecules. Explain your answer. A. GGCGCACC B. TATTGTCT C. GACTCCTG D. CTAACTGG
The order in which the DNA molecules would denature as the temperature increases is: 1—B; 2—D; 3—C; 4—A All the DNA molecules are the same length, so only the A + T and G + C content determine their relative Tm. Molecules with higher G + C content will be more stable than molecules with a high A + T content. This is because there are three hydrogen bonds between each G-C base pair but only two between each A-T base pair. More energy (heat) is required to disrupt a larger number of hydrogen bonds.
Mitotic chromosomes are _____ times more compact than a DNA molecule in its extended form. (a) 10,000 (b) 100,000 (c) 1000 (d) 100
(a) 10,000
Many of the breakthroughs in modern biology came after Watson and Crick published their model of DNA in 1953. In what decade did scientists first identify chromosomes? (a) 1880s (b) 1920s (c) 1940s (d) 1780s
(a) 1880s
Several experiments were required to demonstrate how traits are inherited. Which scientist or team of scientists first demonstrated that cells contain some component that can be transferred to a new population of cells and permanently cause changes in the new cells? (a) Griffith (b) Watson and Crick (c) Avery, MacLeod, and McCarty (d) Hershey and Chase
(a) Griffith
The classic "beads-on-a-string" structure is the most decondensed chromatin structure possible and is produced experimentally. Which chromatin components are not retained when this structure is generated? (a) linker histones (b) linker DNA (c) nucleosome core particles (d) core histones
(a) linker histones
Methylation and acetylation are common changes made to histone H3, and the specific combination of these changes is sometimes referred to as the "histone code." Which of the following patterns will probably lead to gene silencing? (a) lysine 9 methylation (b) lysine 4 methylation and lysine 9 acetylation (c) lysine 14 acetylation (d) lysine 9 acetylation and lysine 14 acetylation
(a) lysine 9 methylation
The images of chromosomes we typically see are isolated from mitotic cells. These mitotic chromosomes are in the most highly condensed form. Interphase cells contain chromosomes that are less densely packed and __________________________. (a) occupy discrete territories in the nucleus (b) share the same nuclear territory as their homolog (c) are restricted to the nucleolus (d) are completely tangled with other chromosomes
(a) occupy discrete territories in the nucleus
The DNA from two different species can often be distinguished by a difference in the ______________________. (a) ratio of A+T to G+C (b) ratio of A+G to C+T (c) ratio of sugar to phosphate (d) presence of bases other than A, G, C, & T
(a) ratio of A+T to G+C
Interphase chromosomes are about______ times less compact than mitotic chromosomes, but still are about______ times more compact than a DNA molecule in its extended form. (a) 10; 1000 (b) 20; 500 (c) 5; 2000 (d) 50; 200
(b) 20; 500
Mitotic chromosomes were first visualized in the 1880s with the use of very simple tools: a basic light microscope and some dyes. Which of the following characteristics of mitotic chromosomes reflects how they were named? (a) motion (b) color (c) shape (d) location
(b) color
Stepwise condensation of linear DNA happens in five different packing processes. Which of the following four processes has a direct requirement for histone H1? (a) formation of "beads-on-a-string" (b) formation of the 30 nm fiber (c) looping of the 30 nm fiber (d) packing of loops to form interphase chromosomes
(b) formation of the 30 nm fiber
The N-terminal tail of histone H3 can be extensively modified, and depending on the number, location, and combination of these modifications, these changes may promote the formation of heterochromatin. What is the result of heterochromatin formation? (a) increase in gene expression (b) gene silencing (c) recruitment of remodeling complexes (d) displacement of histone H1
(b) gene silencing
The manner in which a gene sequence is related to its respective protein sequence is referred to as the _________ code. (a) protein (b) genetic (c) translational (d) expression
(b) genetic
Nucleosomes are formed when DNA wraps _____ times around the histone octamer in a ______ coil. (a) 2.0; right-handed (b) 2.5; left-handed (c) 1.7; left-handed (d) 1.3; right-handed
(c) 1.7; left-handed
The core histones are small, basic proteins that have a globular domain at the C-terminus and a long extended conformation at the N-terminus. Which of the following is not true of the N terminal "tail" of these histones? (a) It is subject to covalent modifications, (b) It extends out of the nucleosome core. (c) It binds to DNA in a sequence-specific manner. (d) It helps DNA pack tightly.
(c) It binds to DNA in a sequence-specific manner.
When there is a well-established segment of heterochromatin on an interphase chromosome, there is usually a special barrier sequence that prevents the heterochromatin from expanding along the entire chromosome. Gene A, which is normally expressed, has been moved by DNA recombination near an area of heterochromatin. None of the daughter cells produced after this recombination event express gene A, even though its DNA sequence is unchanged. What is this the best way to describe what has happened to the function of gene A in these cells? (a) barrier destruction (b) heterochromatization (c) epigenetic inheritance (d) euchromatin depletion
(c) epigenetic inheritance
The process of sorting human chromosomes pairs by size and morphology is called karyotyping. A modern method employed for karyotyping is called chromosome painting. How are individual chromosomes "painted"? (a) with a laser (b) using fluorescent antibodies (c) using fluorescent DNA molecules (d) using green fluorescent protein
(c) using fluorescent DNA molecules
Although the chromatin structure of interphase and mitotic chromosomes is very compact, DNA-binding proteins and protein complexes must be able to gain access to the DNA molecule. Chromatin-remodeling complexes provide this access by _________________. (a) recruiting other enzymes (b) modifying the N-terminal tails of core histones (c) using the energy of ATP hydrolysis to move nucleosomes (d) denaturing the DNA by interfering with hydrogen-bonding between base pairs
(c) using the energy of ATP hydrolysis to move nucleosomes
The human genome has enough DNA to stretch more than 2 m. However, this DNA is not contained in a single molecule; it is divided into linear segments and packaged into structures called chromosomes. What is the total number of chromosomes found in each of the somatic cells in your body? (a) 22 (b) 23 (c) 44 (d) 46
(d) 46
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
(d) 5 -AAGCGCTT-3
The octameric histone core is composed of four different histone proteins, assembled in a stepwise manner. Once the core octamer has been formed, DNA wraps around it to form a nucleosome core particle. Which of the following histone proteins does not form part of the octameric core? (a) H4 (b) H2A (c) H3 (d) H1
(d) H1
Several experiments were required to demonstrate how traits are inherited. Which scientist or team of scientists obtained definitive results demonstrating that DNA is the genetic molecule? (a) Griffith (b) Watson (c) Crick (d) Hershey and Chase
(d) Hershey and Chase
The complete set of information found in a given organism's DNA is called its ____________. (a) genetic code (b) coding sequence (c) gene (d) genome
(d) genome
Which of the following chemical groups is not used to construct a DNA molecule? (a) five-carbon sugar (b) phosphate (c) nitrogen-containing base (d) six-carbon sugar
(d) six-carbon sugar
In a DNA double helix, _____________________. (a) the two DNA strands are identical (b) purines pair with purines (c) thymine pairs with cytosine (d) the two DNA strands run antiparallel
(d) the two DNA strands run antiparallel
Given the sequence of one strand of a DNA helix as 5'-GCATTCGTGGGTAG-3', give the sequence of the complementary strand and label the 5' and 3' ends.
5'-CTACCCACGAATGC-3'.
Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. DNA molecules, like proteins, consist of a single, long polymeric chain that is assembled from small monomeric subunits. B. The polarity of a DNA strand results from the polarity of the nucleotide subunits. C. There are five different nucleotides that become incorporated into a DNA strand. D. Hydrogen bonds between each nucleotide hold individual DNA strands together.
A. *False*. DNA is double-stranded. It is actually is made of two polymers that are complementary in sequence. B. *True*. C. *False*. There are four different nucleotides that are used to make a DNA polymer: adenine, thymine, guanine, and cytosine. A fifth nucleotide, uracil, is found exclusively in RNA molecules, replacing thymine nucleotides in the DNA sequence. D. *False*. Nucleotides are linked covalently through phosphodiester bonds. Hydrogen-bonding between nucleotides from opposite strands holds the DNA molecule together.
Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Comparing the relative number of chromosome pairs is a good way to determine whether two species are closely related. B. Chromosomes exist at different levels of condensation, depending on the stage of the cell cycle. C. Eucaryotic chromosomes contain many different sites where DNA replication can be initiated. D. The telomere is a specialized DNA sequence where microtubules from the mitotic spindle attach to the chromosome so that duplicate copies move to opposite ends of the dividing cell.
A. *False*. There are several examples of closely related species that have a drastically different number of chromosome pairs. Two related species of deer—Chinese and Indian muntjac—have 23 and 3, respectively. B. *True*. C. *True*. D. *False*. The telomere is a specialized DNA sequence, but not for the attachment of spindle microtubules. Telomeres form special caps that stabilize the ends of linear chromosomes.
Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Each strand of DNA contains all the information needed to create a new double- stranded DNA molecule with the same sequence information. B. All functional DNA sequences inside a cell code for protein products. C. Gene expression is the process of duplicating genes during DNA replication. D. Gene sequences correspond exactly to the respective protein sequences produced from them.
A. *True*. B. *False*. Some sequences encode only RNA molecules, some bind to specific regulatory proteins, and others are sites where specific chromosomal protein structures are built (for example, centromeric and telomeric DNA). C. *False*. Gene expression is the process of going from gene sequence to RNA sequence, to protein sequence. D. *False*. This statement is false for two reasons. First, genes often contain intron sequences. Second, genes always contain nucleotides flanking the protein-coding sequences that are required for the regulation of transcription and translation.
The number of cells in an average-sized adult human is on the order of 1014. Use this information, and the estimate that the length of DNA contained in each cell is 2 m, to do the following calculations (look up the necessary distances and show your working): A. Over how many miles would the total DNA from the average human stretch? B. How many times would the total DNA from the average human wrap around the planet Earth at the Equator? C. How many times would the total DNA from the average human stretch from Earth to the Sun and back? D. How many times would the total DNA from the average human stretch from the Earth to Pluto and back?
A. 2 × 1014 m = 124,274,238,447 miles. B. The Earth's circumference at the Equator is 7,926 miles. The length of DNA from the average human body could wrap around the Earth 15,678,759 times. C. The average distance from the Earth to the Sun is 93,000,000 miles. So, the round-trip distance is 186,000,000 miles. The length of DNA from the average human body could stretch from the Earth to the Sun and back 668 times. D. The distance from the Earth to Pluto is, on average, about 39 × 93,000,000 miles. The length of DNA from the average human body could stretch from the Earth to Pluto and back 36 times.
A. Define a gene. B. Consider two different species of yeast that have similar genome sizes. Is it likely that they contain the same number of genes? A similar number of chromosomes? C. 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?
A. 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). B. 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 roughly 400 million years of evolution, and both have a genome of 14 million base pairs. Yet Sc has 6500 genes packaged into 16 chromosomes and Sp has 4800 genes in 3 chromosomes. C. 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.
A. 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. B. On average, how often would the nucleotide sequence CGATTG be expected to occur in a DNA strand 4000 bases long? Explain your reasoning.
A. Because 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 signals. A code of three consecutive nucleotides has 64 (43) different members and thus can easily accommodate the 20 amino acids plus a signal to stop protein synthesis. B. Because 46 (= 4096) different sequences of six nucleotides can occur in DNA, any given sequence of six nucleotides would be expected to occur on average once in a DNA strand 4000 bases long, assuming a random distribution of sequences.
Consider the structure of the DNA double helix. A. 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. B. 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 material." What did they mean?
A. It is better to separate the strands 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. B. 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.
For each of the following sentences, choose one of the options enclosed in square brackets to make a correct statement about nucleosomes. A. Nucleosomes are present in [procaryotic/eucaryotic] chromosomes, but not in [procaryotic/eucaryotic] chromosomes. B. A nucleosome contains two molecules each of histones [H1 and H2A/H2A and H2B] as well as of histones H3 and H4. C. A nucleosome core particle contains a core of histone with DNA wrapped around it approximately [twice/three times/four times]. D. Nucleosomes are aided in their formation by the high proportion of [acidic/basic/polar] amino acids in histone proteins. E. Nucleosome formation compacts the DNA into approximately [one-third/one- hundredth/one-thousandth] of its original length.
A. Nucleosomes are present in *eucaryotic* chromosomes, but not in *procaryotic* chromosomes. B. A nucleosome contains two molecules each of histones *H2A and H2B* as well as of histones H3 and H4. C. A nucleosome core particle contains a core of histone with DNA wrapped around it approximately *twice*. D. Nucleosomes are aided in their formation by the high proportion of *basic* amino acids in histone proteins. E. Nucleosome formation compacts the DNA into approximately *one-third* of its original length.
The human genome comprises 23 pairs of chromosomes found in nearly every cell in the body. Answer the quantitative questions below by choosing one of the numbers in the following list: 23 69 >200 46 92 >109 A. How many centromeres are in each cell? What is the main function of the centromere? B. How many telomeres are in each cell? What is their main function? C. How many replication origins are in each cell? What is their main function?
A. There are 46 centromeres per cell, one on each chromosome. The centromeres have a key role in the distribution of chromosomes to daughter cells during mitosis. B. There are 92 telomeres per cell, two 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. C. There are far more than 200 replication origins in a human cell, probably about 10,000. These DNA sequences direct the initiation of DNA synthesis needed to replicate chromosomes.
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. A. Do you think Tm is a constant, or can it depend on other small molecules in the solution? Do you think high salt concentrations increase, decrease, or have no effect on Tm? B. Under standard conditions, the expected melting temperature in degrees Celsius can be calculated from the equation Tm = 59.9 + 0.41 [%(G + C)] - [675/length of duplex]. Does the Tm increase or decrease if there are more G + C (and thus fewer A + T) base pairs? Does the Tm increase or decrease as the length of DNA increases? Why? C. Calculate the predicted Tm for a stretch of double helix that is 100 nucleotides long and contains 50% G + C content.
A. 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 each other less strongly. Thus, a high salt concentration stabilizes the duplex and increases the melting temperature. B. 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, whereas an A-T base pair contributes only two. C. 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.
Using terms from the list below, fill in the blanks in the following brief description of the experiment with Streptococcus pneumoniae that identified which biological molecule carries heritable genetic information. Some terms may be used more than once. Cell-free extracts from S-strain cells of S. pneumoniae were fractionated to __________________ DNA, RNA, protein, and other cell components. Each fraction was then mixed with __________________ cells of S. pneumoniae. Its ability to change these into cells with __________________ properties resembling the __________________ cells was tested by injecting the mixture into mice. Only the fraction containing __________________ was able to __________________ the __________________ cells to __________________ (or __________________ ) cells that could kill mice. carbohydrate DNA identify label lipid purify nonpathogenic pathogenic R-strain RNA S-strain transform
Cell-free extracts from S-strain cells of S. pneumoniae were fractionated to *purify* DNA, RNA, protein, and other cell components. Each fraction was then mixed with *R-strain* cells of S. pneumoniae. Its ability to change these into cells with *pathogenic* properties resembling the *S-strain* cells was tested by injecting the mixture into mice. Only the fraction containing *DNA* was able to *transform* the *R-strain* cells to *pathogenic* (or *S-strain*) cells that could kill mice.
Explain the differences between chromosome painting and the older, more traditional method of staining chromosomes being prepared for karyotyping. Highlight the way in which each method identifies chromosomes by the unique sequences they contain.
Chromosome painting relies on the specificity of DNA complementarity. Because unique sequences for each chromosome are known, short DNA molecules matching a set of these sites can be designed for each chromosome. Each set is labeled with a specific combination of fluorescent dyes and then allowed to hybridize (form base pairs) with the two homologous chromosomes that contain the unique sequences being targeted. Giemsa stain is a nonfluorescent dye that has a high affinity for DNA, and specifically accumulates in regions that are rich in A-T nucleotide pairs. This dye produces a pattern of dark and light bands, which differ for each chromosome on the basis of the distribution of A-T-rich regions.
For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. 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 __________________ that help package the DNA in an orderly manner so it can fit in the small space delimited by the __________________. The structure of the DNA-protein complex, called __________________, is highly __________________ over time. 10,000 100 1000 cell cycle cell wall chromatin chromosome different DNA dynamic interphase lipids mitosis nucleolus proteins nuclear envelope static similar
Each chromosome is a single molecule of *DNA* whose extraordinarily long length can be compacted by as much as *1000*-fold during *interphase* and tenfold more during *mitosis*. This is accomplished by binding to *proteins* that help package the DNA in an orderly manner so it can fit in the small space delimited by the *nuclear envelope*. The structure of the DNA-protein complex, called *chromatin*, is highly *dynamic* over time.
