Ch5.doc

CHAPTER 5 DNA AND CHROMOSOMES 

2009 Garland Science Publishing

The Structure and Function of DNA 5-1

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 nonpathogenic pathogenic purify

R-strain RNA S-strain transform

5-2

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

5-3

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

5-4

In a DNA double helix, _____________________. (a) the two DNA strands are identical

(b) (c) (d)

purines pair with purines thymine pairs with cytosine the two DNA strands run antiparallel

5-5

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.

5-6

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

5-7

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

5-8

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

5-9

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′

5-10

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) 5-11

presence of bases other than A, G, C, and T

For a better understanding of DNA structure, it helps to be able to compare physical characteristics evident from a side view of double-stranded DNA with those of individual base pairs. A. Use brackets to designate the major and minor grooves on Figure Q5-11A and shade in the surface that will be exposed in the major grove in Figure Q5-11B. B. If base pairs were aligned and stacked directly on top of each other, the major and minor grooves would be linear depressions all along the DNA. Explain why this is not the actual conformation of a DNA molecule.

Figure Q5-11 5-12

Which DNA base pair is represented in Figure Q5-12? (a) A-T (b) T-A (c) G-C (d) C-G

Figure Q5-12 5-13

Use the terms listed to fill in the blanks in Figure Q5-13. A. A-T base pair B. G-C base pair C. deoxyribose D. phosphodiester bonds E. purine base F. pyrimidine base

Figure Q5-13 5-14

The structures of the four bases in DNA are given in Figure Q5-14.

Figure Q5-14 A. B.

Which are purines and which are pyrimidines? Which bases pair with each other in double-stranded DNA?

5-15

Using the structures in Figure Q5-15 as a guide, sketch the hydrogen bonds between the base pairs in DNA. Hint: The bases in the figure are all drawn with the –NH– that attaches to the sugar at the bottom of the structure.

5-16

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 doublestranded DNA molecules. Explain your answer. A. GGCGCACC B. TATTGTCT C. GACTCCTG D. CTAACTGG

5-17

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 doublestranded 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.

5-18

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

5-19

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

5-20

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.

5-21

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.

5-22

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?

5-23

A.

B.

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. On average, how often would the nucleotide sequence CGATTG be expected to occur in a DNA strand 4000 bases long? Explain your reasoning.

The Structure of Eucaryotic Chromosomes 5-24

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

5-25

A. B. C.

extended homologous hybridization karyotype

kinetochore nonhomologous

Define a gene. 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? 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?

5-26

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

5-27

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?

5-28

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

5-29

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 46 A. B. C.

69 92

>200 >109

How many centromeres are in each cell? What is the main function of the centromere? How many telomeres are in each cell? What is their main function? How many replication origins are in each cell? What is their main function?

5-30

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.

5-31

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.

5-32

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 nuclear envelope nucleolus proteins similar static

5-33

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

5-34

Figure Q5-34 clearly depicts the nucleolus, a nuclear structure that looks like large dark region when stained. The other dark speckled regions in this image are the locations of particularly compact chromosomal segments called ____________. (a) euchromatin (b) heterochromatin (c) nuclear pores (d) nucleosomes

Figure Q5-34 5-35

Mitotic chromosomes are _____ times more compact than a DNA molecule in its extended form. (a) 10,000 (b) 100,000

(c) (d)

1000 100

5-36

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

5-37

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/onehundredth/one-thousandth] of its original length.

5-38

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

5-39

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

5-40

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

5-41

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

5-42

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.

5-43

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

5-44

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 Regulation of Chromosome Structure 5-45

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 5-46

You are studying a newly identified chromatin-remodeling complex, which you call NICRC. You decide to run an in vitro experiment to characterize the activity of the purified complex. Your molecular toolbox includes: (1) a 400-base-pair DNA molecule that has a single recognition site for the restriction endonuclease EcoRI, an enzyme that cleaves internal sites on double-stranded DNA (dsDNA); (2) purified EcoRI enzyme; (3) purified DNase I, a DNA endonuclease that will cleave dsDNA at nonspecific sites if they are exposed; and (4) core octamer histones. You are able to assemble core nucleosomes on this DNA template and test for NICRC activity. Figure Q5-46A illustrates the DNA template used and indicates both the location of the EcoRI cleavage site and the size of the DNA fragments that are produced when it cuts. Figure Q5-46B illustrates how the DNA molecules in your experiment looked after separation according to size by using gel electrophoresis. Your experiment had a total of six samples, each of which was treated according to the legend below the gel. The sizes of the DNA fragments observed are indicated on the left side of the gel.

Figure Q5-46 A

Explain the results in lanes 1–4 and why it is important to have this information before you begin to test your remodeling complex.

B.

What can you conclude about your purified remodeling complex from the results in lanes 5 and 6?

5-47

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

5-48

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

5-49

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

5-50

Your friend is working in a lab to study how yeast cells adapt to growth on different carbon sources. He grew half of his cells in the presence of glucose and the other half in the presence of galactose. Then he harvested the cells and isolated their DNA with a gentle procedure that leaves nucleosomes and some higher-order chromatin structures intact. He treated the DNA briefly with a low concentration of M-nuclease, a special enzyme that easily degrades protein-free stretches of DNA. After removing all the proteins, he separated the resulting DNA on the basis of length. Finally, he used a procedure to visualize only those DNA fragments from a region near a particular gene called Sweetie or another gene called Salty. The separated DNA fragments are shown in Figure Q5-50. Each vertical column, called a lane, is from a different sample. DNA spots near the top of the figure represent DNA molecules that are longer than those near the bottom. Darker spots contain more DNA than fainter spots. The lanes are as follows: 1. 2.

“marker” containing known DNA fragments of indicated lengths cells grown in glucose, DNA visualized near Sweetie gene

3. 4. 5.

cells grown in galactose, DNA visualized near Sweetie gene cells grown in glucose, DNA visualized near Salty gene cells grown in galactose, DNA visualized near Salty gene

Figure Q5-50 A. B. C.

D. E.

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? What are the spots with longer lengths? Why is there a ladder of spots? 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 to change the pattern between lanes 2 and 3? What kinds of enzyme might have been involved in changing the chromatin structure between lanes 2 lane 3? Do you think that gene expression of Sweetie is higher, lower, or the same in galactose compared to glucose? What about Salty?