1. 24| Genes and Chromosomes
© 2017 W. H. Freeman and Company

2. Management and Expression of Genetic Information
Previous chapters dealt with:
metabolic pathways, in which the chemical structures of small molecules were modified by enzymes
signal transduction pathways, in which interactions of ligands with receptor proteins caused physiological responses
The following chapters deal with:
information pathways, in which genetic information stored as the nucleotide sequence is maintained and expressed yielding many of the macromolecules previously discussed or enzymes needed for their synthesis

3. The “Central Dogma” of How Information Flows in Biological Systems
PART III UNNUMBERED FIGURE. The central dogma of molecular biology, showing the general pathways of information flow via replication, transcription, and translation. The term “dogma” is a misnomer and is retained for historical reasons only. Introduced by Francis Crick at a time when little evidence supported these ideas, the dogma has become a well-established principle.

4. The Central Dogma of Molecular Biology
The discovery of the double-helical structure of DNA in 1953 laid a foundation to thinking of biomolecules as carriers of information.
It was understood by 1950 that proteins are catalysts, but their role in information transfer was unclear.
Francis Crick proposed in 1956 that “Once information has got into a protein it can’t get out again.”
The central dogma was proposed by Francis Crick at the time when there was little evidence to support it, hence the “dogma.”

5. Information Flow According to the Central Dogma
Information from parental DNA is copied to daughter DNA with high fidelity via DNA replication.
RNA is synthesized using DNA as a template during transcription.
Proteins are synthesized based on the information stored in ribonucleotide triplets in RNA during translation.
Caveat: Viruses are able to make RNA and DNA using RNA as a template in reverse transcription.

6. The “Central Dogma” of How Information Flows in Biological Systems
PART III UNNUMBERED FIGURE. The central dogma of molecular biology, showing the general pathways of information flow via replication, transcription, and translation. The term “dogma” is a misnomer and is retained for historical reasons only. Introduced by Francis Crick at a time when little evidence supported these ideas, the dogma has become a well-established principle.

7. Understanding of Genes Has Evolved
Historically, a gene was “something” responsible for a characteristic, or phenotype.
Beadle and Tatum, through mutation studies, defined a gene as something that coded for an enzyme (one gene  one enzyme).
Now genes are defined as segments of DNA that code for peptides and RNA.
different from regulatory sequences
DNA can be expressed differently to yield different products (one gene  different products).

8. CHAPTER 24 Genes and Chromosomes
Learning goals:
Organization of information in chromosomes
DNA supercoiling
Structure of the chromosome

9. DNA Is a Very Large Macromolecule
The linear dimensions of DNA are much bigger than the virions or cells that contain them.
bacteriophage T4: ~0.2 m long and 0.1 m wide
T4 DNA: ~60 m long
So DNA in a virion or cell is organized into compact forms, typically via coiling and association with proteins.

10. Linearized DNA from Bacteriophage T2
FIGURE 24–1 Bacteriophage T2 protein coat surrounded by its single, linear molecule of DNA. The DNA was released by lysing the bacteriophage particle in distilled water and allowing the DNA to spread on the water surface. An undamaged T2 bacteriophage particle consists of a head structure that tapers to a tail by which the bacteriophage attaches itself to the outer surface of a bacterial cell. All the DNA shown in this electron micrograph is normally packaged inside the phage head.

11. Molecular Coding of Protein Sequence Information
In transcription, one strand of double-stranded DNA acts as the molecular template for RNA synthesis (DNA  messenger RNA).
Three nucleotides code for one “codon.”
In translation, the triplets of nucleotides in mRNA bind to complementary triplets in tRNA.
The tRNA molecules carry an amino acid associated with the particular triplet.
Amino acids are then assembled in peptide chains.
Protein sequence determines its biological function.

12. How DNA Codes for mRNA That Then Codes for the Amino Acid Sequence
FIGURE 24–2 Colinearity of the coding nucleotide sequences of DNA and mRNA and the amino acid sequence of a polypeptide chain. The triplets of nucleotide units in DNA determine the amino acids in a protein through the intermediary mRNA. One of the DNA strands serves as a template for synthesis of mRNA, which has nucleotide triplets (codons) complementary to those of the DNA. In some bacterial and many eukaryotic genes, coding sequences are interrupted at intervals by regions of noncoding sequences (called introns).

13. How Many Genes per Organism?
E. coli (single circular chromosome) – 4,639,675 bp  ~4300 genes for proteins and ~157genes for catalytic or structural RNAs
Human (24 discrete chromosomes) – 3.1 billion bp  ~20,000 genes

14. Many Viral Genomes Are RNA
Many viruses: only RNA or DNA surrounded by protein coat
They use the host’s genes when they infect a plant, animal, or bacterium.
RNA genomes may be small and single-stranded.
HIV: 9000 bp
phage Q: 4220 bp
Genomes may change form from circular to linear, and so on, during the life cycle.

15. Bacterial Genomes Are Double-Stranded Circles
E.coli: 4,639,675 bp
850 longer than the cell!
Bacteria also contain extra-chromosomal, double-stranded circular plasmids.
usually ~2000–10,000 bp, but can be 400,000 bp
swapped easily between bacteria
no essential genes, but often encode genes that degrade antibiotics
plasmid exchange: one way bacteria acquire antibiotic resistance
TABLE 24-1
The Sizes of DNA and Viral Particles for Some Bacterial Viruses (Bacteriophages)
Virus
Size of viral DNA (bp)
Length of viral DNA (nm)
Long dimension of viral particles (nm)
fX174
5,386
1,939 25 T7
39,936
14,377 78
λ (lambda)
48,502
17,460
190 T4
168,889
60,800
210
Note: Data on size of DNA are for the replicative form (double-standard). The contour length is calculated assuming that each base pair occupies a length of 3.4 Å (see Fig. 8-13).

16. Length of E. Coli DNA Relative to Length of Cell
FIGURE 24–3 The length of the E. coli chromosome (1.7 mm) depicted in linear form relative to the length of a typical E. coli cell (2 μm).

17. DNA from Lysed E. Coli Cell Containing Plasmids
FIGURE 24-4 DNA from a lysed E. coli cell. In this electron micrograph several small, circular plasmid DNAs are indicated by white arrows. The black spots and white specks are artifacts of the preparation.

18. Eukaryote DNA Is in Multiple Discrete Chromosomes
The number varies with species.
Human somatic (non-sex) cells have 46 chromosomes.
22 pairs (diploid) plus X and Y
amounts to ~2 m of DNA
length of each pair varies

19. Eukaryotic Chromosome
FIGURE 24–5a Eukaryotic chromosomes. (a) A pair of linked and condensed sister chromatids of a human chromosome. Eukaryotic chromosomes are in this state after replication at metaphase during mitosis.

20. Complete Set of Human Chromosomes (Male)
FIGURE 24–5b Eukaryotic chromosomes. (b) A complete set of chromosomes from a leukocyte from one of the authors. There are 46 chromosomes in every normal human somatic cell.

21. Number of chromosomesa Approximate number of genes
TABLE 24-2
DNA, Gene, and Chromosome Content in Some Genomes
Total DNA (bp)
Number of chromosomesa
Approximate number of genes
Escherichia coli K12 (bacterium)
4,641,652 1
4,494b
Saccharomyces cerevisiae (yeast)
12,157,105
16c
6,340b
Caenorhabditis elegans (nematode)
90,269,800
12d
23,000
Arabidopsis thaliana (plant)
119,186,200 10
33,000
Drosophila melanogaster (fruit fly)
120,367,260 18
20,000
Oryza sativa (rice)
480,000,000 24
57,000
Mus musculus (mouse)
2,634,266,500 40
27,000
Homo sapiens (human)
3,070,128,600 46
Note: This information is constantly being refined. For the most current information, consult the websites for the individual genome projects.
aThe diploid chromosomes number is given for all eukaryotes except yeast.
bIncludes known RNA-coding genes.
cHaploid chromosomes number. Wild yeast strains generally have eight (octoploid) or more sets of these chromosomes.
dNumber for females, with two X chromosomes. Males have an X but no Y, thus 11 chromosomes in all.

22. Mitochondria and Chloroplasts Also Have DNA
Double-stranded circles
Human mitochondrial DNA (mtDNA)
16,569 bp
~2–10 copies per mitochondrion
Plant mtDNA
200,000–2,500,000 bp
Chloroplast DNA (cpDNA)
120,000–160,000 bp

23. Mitochondrial DNA
It codes for mitochondrial rRNAs, tRNAs, and some of the mitochondrial specific proteins.
Most mitochondrial proteins (at least 95%) are encoded by nuclear genes.

24. Mitochondrion
FIGURE 24–6 A dividing mitochondrion. Some mitochondrial proteins and RNAs are encoded by one of the copies of the mitochondrial DNA (none of which are visible here). The DNA (mtDNA) is replicated each time the mitochondrion divides, before cell division.

25. DNA, Chromosomes, Genes, and Complexity
Neither the total length of DNA nor the number of chromosomes correlates strongly with the complexity of an organism .
Dogs and coyotes have 78 chromosomes.
Amphibians have much more DNA than humans do.
Plants have more genes than humans do.
The correlation between genome size and complexity is poor because most of eukaryotic DNA is noncoding.
Recent experimental work by Craig Venter suggests that a living organism could get by with less than 400 genes.

26. DNA Is Packaged with Proteins
Viral genomic DNA may be associated with capsid proteins.
Prokaryotic DNA is associated with proteins in the nucleoid.
Eukaryotic DNA is organized with proteins into a complex called chromatin.

27. Composition of the Human Genome
Notice that only a small fraction (1.5%) of the total genome encodes for proteins.
The biological significance of noncoding sequences is not entirely clear.
Some DNA regions directly participate in the regulation of gene expression (promoters, termination signals, etc.).
Some DNA encodes for small regulatory RNA with poorly understood functions.
Some DNA may be junk (pieces of unwanted genes, remnants of viral infections).

28. Eukaryotic Genes Contain Intervening Sequences (Introns)
Exons are expressed sequences (translated into amino acid sequence).
Exons account for only 1.5% of human DNA!
Introns are regions of genes that are transcribed but not translated.
They do not encode polypeptide sequence.
Introns are removed after transcription and the exon mRNA sequences are spliced together.
 creates “mature transcripts”

29. Introns in Two Eukaryotic Genes
FIGURE 24–7 Introns in two eukaryotic genes. The gene for ovalbumin has seven introns (A to G), splitting the coding sequences into eight exons (L, and 1 to 7). The gene for the β subunit of hemoglobin has two introns and three exons, including one intron that alone contains more than half the base pairs of the gene.

30. Some Bacterial Genomes Also Contain Introns
Until 1993, scientists thought that introns appeared only in eukaryotes.
About 25% of sequenced bacterial genomes show presence of introns.
Introns in bacterial chromosome do not interrupt protein-coding sequences; they interrupt mainly tRNA sequences.
Introns in phage genomes within bacteria interrupt protein-coding sequences.
Many bacterial introns encode catalytic RNA sequences that have the ability to insert and reverse transcribe themselves into the genomic DNA.

31. Transposons Are Sequences That Can Move Within the Genome
The eukaryotic genome is not completely static.
Sequences called transposons can move around within the genome of a single cell.
The ends of transposons contain terminal repeats.
These repeats hybridize with complementary regions of target DNA during insertion.
Transposons account for ~50% of the human genome.

32. Eukaryotes Also Contain Highly Repetitive DNA or Simple Sequence Repeats (SSRs)
Short sequences of ~10 bp or less
Repeated millions of times
Also known as “satellite” DNA
because when fragmented and centrifuged, the DNA separates into a discrete “satellite” band
Associated with centromeres and telomeres

33. Telomeres and Centromeres in a Yeast Chromosome
FIGURE 24-8 Important structural elements of a yeast chromosome.

34. Centromere Sequences Are Where Proteins Attach During Mitosis
Region where the two daughter chromosomes are held together during mitosis
that is, after DNA replication but before cell division
Essential for equal distribution of chromosome sets to daughter cells
Have AT-rich repeated sequences of ~130 bp

35. Telomere Sequences Cap the Ends of Eukaryotic Chromosomes
May form special loop structures to keep DNA ends from unraveling
contain multiple repeats with general sequence
(TxGy)n
(AxCy)n , where n = 1500 or more in mammals
added by enzyme telomerase

36. TABLE 24-3 Telomere Sequences Organism Telomere repeat sequence
Homo sapiens (human)
(TTAGGG)n
Tetrahymena thermophila (ciliated protozoan)
(TTGGGG)n
Saccharomyces cerevisiae (yeast)
((TG)1–3(TG)2–3)n
Arabidopsis thaliana (plant)
(TTTAGGG)n

37. Telomeres Are Associated with Cellular Aging
In many tissues, telomeres are shortened after each round of replication.
Thus, the cellular DNA “ages.”
Normal human cells divide about 52 times before losing the ability to divide again (Hayflick limit).

38. DNA Supercoiling DNA in the cell must be organized to allow:
packing of large DNA molecules within the cells
access of proteins to read the information in DNA sequence
There are several levels of organization, one of which is the supercoiling of the double-stranded DNA helix.

39. Helical Supercoils
FIGURE 24–9 Supercoils. A typical phone cord is coiled like a DNA helix, and the coiled cord can itself coil in a supercoil. The illustration is especially appropriate because an examination of phone cords helped lead Jerome Vinograd and his colleagues to the insight that many properties of small circular DNAs can be explained by supercoiling. They first detected DNA supercoiling—in small circular viral DNAs—in 1965.

40. Supercoiling Is the Coiling of a Coil
Nonsupercoiled DNA is called relaxed.
Many circular DNAs are supercoiled.
Supercoiling has great influence on transcription and replication of DNA.
Supercoiling can be highly regulated.

41. Closing DNA in a Loop Introduces Supercoiling
FIGURE 24–10 Supercoiling of DNA. When the axis of the DNA double helix is coiled on itself, it forms a new helix (superhelix). The DNA superhelix is usually called a supercoil.

42. The Effects of Replication and Transcription on DNA Supercoiling
FIGURE 24–11 The effects of replication and transcription on DNA supercoiling. Because DNA is a double-helical structure, strand separation leads to added stress and supercoiling if the DNA is constrained (not free to rotate) ahead of the strand separation. (a) The general effect can be illustrated by twisting two strands of a rubber band about each other to form a double helix. If one end is constrained, separating the two strands at the other end will lead to twisting. (b) In a DNA molecule, the progress of a DNA polymerase or RNA polymerase (as shown here) along the DNA involves separation of the strands. As a result, the DNA becomes overwound ahead of the enzyme (upstream) and underwound behind it (downstream). Red arrows indicate the direction of winding.

43. Most Cellular DNA Is Underwound
Normal B-form, relaxed DNA: 10.5 bp/turn
Closed circular DNA is rarely relaxed.
The strain induces supercoiling.
The strain is due to fewer helical turns (underwinding).
Underwinding makes later separation of the strands easier.
Linear DNA is underwound with the help of proteins to prevent strands from rotating

44. Relaxed and Increasingly Supercoiled Plasmid DNA
FIGURE 24–12 Relaxed and supercoiled plasmid DNAs. The molecule in the leftmost electron micrograph is relaxed; the degree of supercoiling increases from left to right.

45. Effects of DNA Underwinding
FIGURE 24–13 Effects of DNA underwinding. (a) A segment of DNA in a closed-circular molecule, 84 bp long, in its relaxed form with eight helical turns. (b) Removal of one turn induces structural strain. (c) The strain is generally accommodated by formation of a supercoil. (d) DNA underwinding also makes the separation of strands somewhat easier. In principle, each turn of underwinding should facilitate strand separation over about 10 bp, as shown. However, the hydrogen-bonded base pairs would generally preclude strand separation over such a short distance, and the effect becomes important only for longer DNAs and higher levels of DNA underwinding.

46. Linking Number (Lk) Describes Supercoiling
In circular DNA, changing the helical turns requires breaking a strand transiently.
Linking number in relaxed DNA:
Lk = #bp  #bp/turn
Example: Relaxed circular dsDNA of 2100 bp in the B form (10.5 bp/turn) has
Lk = 2100 bp  10.5/turn = 200
Lk is an integer for closed-circular DNA and is (+), reflecting a right-handed helix.

47. Lk Is the Number of Times a Strand Penetrates a Surface
FIGURE 24–14 Linking number, Lk. Here, as usual, each blue ribbon represents one strand of a double-stranded DNA molecule. For the molecule in (a), Lk 5 1. For the molecule in (b), Lk 5 6. One of the strands in (b) is kept untwisted for illustrative purposes, to define the border of an imaginary surface (shaded blue). The number of times the twisting strand penetrates this surface provides a rigorous definition of linking number.

48. Lk Applied to Closed-Circular DNA
FIGURE 24–15 Linking number applied to closed-circular DNA molecules. A 2,100 bp circular DNA is shown in three forms: (a) relaxed, Lk 5 200; (b) relaxed with a nick (break) in one strand, Lk undefined; and (c) underwound by two turns, Lk The underwound molecule generally exists as a supercoiled molecule, but underwinding also facilitates the separation of DNA strands.

49. Changes in Lk Are Useful for Describing Supercoiling
Consider a relaxed DNA of 2100 bp:
Lk0 = 200
Underwind by removing two helical turns:
Lk = 198
Lk = 198 – 200 = –2

50. Superhelical Density, 

51. Negative and Positive Supercoils
FIGURE 24–16 Negative and positive supercoils. For the relaxed DNA molecule of Figure 24–15a, underwinding or overwinding by two helical turns (Lk or 202) will produce negative or positive supercoiling, respectively. Note that the DNA axis twists in opposite directions in the two cases.

52. Linking Number Can Be Broken Down into Twist (Tw) and Write (Wr)
Lk = Tw + Wr
Twist (Tw) is the # twists or turns of the helix
Writhe (Wr) is the # coils
typically a negative value

53. Underwinding Facilitates Additional DNA Structural Changes
Helps to maintain structure of cruciforms at palindromes (next slide)
Cruciforms rarely occur in relaxed DNA.
Facilitates formation of stretches of left-handed Z form

54. Cruciforms
FIGURE 24–17 Promotion of cruciform structures by DNA underwinding. In principle, cruciforms can form at palindromic sequences (see Fig. 8–19), but they seldom occur in relaxed DNA because the linear DNA accommodates more paired bases than does the cruciform structure. Underwinding of the DNA facilitates the partial strand separation needed to promote cruciform formation at appropriate sequences.

55. Topoisomers Are DNAs That Differ Only in Linking Number
Same # bp, same sequence but different degree of supercoiling
Conversion between topoisomers requires a DNA strand break.
Note that negatively supercoiled DNA (more compact) travels faster in an agarose gel electrophoresis experiment than relaxed or nicked DNA do.

56. Topoisomers in Electrophoresis
FIGURE 24–18 Visualization of topoisomers. In this experiment, all DNA molecules have the same number of base pairs but exhibit some range in the degree of supercoiling. Because supercoiled DNA molecules are more compact than relaxed molecules, they migrate more rapidly during gel electrophoresis. The gels shown here separate topoisomers (moving from top to bottom) over a limited range of superhelical density. In lane 1, highly supercoiled DNA migrates in a single band, even though different topoisomers are probably present. Lanes 2 and 3 illustrate the effect of treating the supercoiled DNA with a type I topoisomerase; the DNA in lane 3 was treated for a longer time than that in lane 2. As the superhelical density of the DNA is reduced to the point where it corresponds to the range in which the gel can resolve individual topoisomers, distinct bands appear. Individual bands in the region indicated by the bracket next to lane 3 each contain DNA circles with the same linking number; the linking number changes by 1 from one band to the next.

57. Topoisomerases Are Enzymes That Change Lk
These enzymes are required for DNA unwinding and rewinding during transcription and replication.
Two major types:
Type I – make a transient cut in one DNA strand, changes Lk by 1
Type II – make a transient cut in both DNA strands, change Lk in steps of 2

58. The Topoisomerases I–IV of E. Coli
Topo I and III are Type I.
remove negative supercoils to relax DNA
increase Lk
use single-stranded breaks
Topo II is called DNA gyrase.
introduces negative supercoils
decreases Lk
uses ATP and double-stranded breaks

59. Type 1 Topoisomerase
MECHANISM FIGURE 24–19 step 1 The type I topoisomerase reaction. Bacterial topoisomerase I increases Lk by breaking one DNA strand, passing the unbroken strand through the break, then resealing the break. Nucleophilic attack by the active-site Tyr residue breaks one DNA strand. The ends are ligated by a second nucleophilic attack. At each step, one high-energy bond replaces another.

60. MECHANISM FIGURE 24–19 step 2 The type I topoisomerase reaction
MECHANISM FIGURE 24–19 step 2 The type I topoisomerase reaction. Bacterial topoisomerase I increases Lk by breaking one DNA strand, passing the unbroken strand through the break, then resealing the break. Nucleophilic attack by the active-site Tyr residue breaks one DNA strand. The ends are ligated by a second nucleophilic attack. At each step, one high-energy bond replaces another.

61. MECHANISM FIGURE 24–19 step 3,4 The type I topoisomerase reaction
MECHANISM FIGURE 24–19 step 3,4 The type I topoisomerase reaction. Bacterial topoisomerase I increases Lk by breaking one DNA strand, passing the unbroken strand through the break, then resealing the break. Nucleophilic attack by the active-site Tyr residue breaks one DNA strand. The ends are ligated by a second nucleophilic attack. At each step, one high-energy bond replaces another.

62. Eukaryotic Topoisomerases Include Topo I, II, II, IV
Topo I and III are Type I (as in E. coli).
Type II topoisomerases include two subfamilies—Type IIA and Type IIB.
can relax both positive and negative supercoils

63. Diversity of DNA Topoisomerases
TABLE 24-4
Diversity in DNA Topoisomerases
Type
Mechanism
Family (defined by structural class)
Domain(s)
Notes IA
Strand passagea
Topoisomerase I
Topoisomerase III
Reverse gyrase
Bacteria, eukaryotes
Archaea, bacteria
Relaxes (–)
Uses ATP to introduce positive supercoils; thermophilic bacteria and archaea only IB
Swivelaseb
Topoisomerase IB
A few bacteria; all eukaryotes IC
Swivelase
Topoisomerase V
Archaea
Methanopyrus only
IIA
Strand passagec
Topoisomerase II (DNA gyrase)
Topoisomerase IIα
Topoisomerase IIβ
Topoisomerase IV
Eukaryotes
Bacteria
Introduces negative supercoils (ATPase)
Relaxes (+ or –)
Decatenased
IIB
Strand passage
Topoisomerase VI
Archaea, bacteria, eukaryotes
Among eukaryotes, plants, algae, and protists only
aSee Figure
bA nick is made in one strand, and the other strand is allowed to rotate to relieve topological strain.
cSee Figure 24-20a.
dSee Figure 24-20b.
Table 24-4 Diversity in DNA Topoisomerases

64. Mechanism of a Eukaryotic Type II Topoisomerase
FIGURE 24–20 Alteration of the linking number by a eukaryotic type IIα topoisomerase. The general mechanism features the passage of one intact duplex DNA segment through a transient double-strand break in another segment. The DNA segment enters and leaves the topoisomerase through gated cavities above and below the bound DNA, which are called the N gate and the C gate. Two ATPs are bound and hydrolyzed during this cycle. The enzyme structure and use of ATP are specific to this reaction.

65. Topoisomerases Are Targets for Antibiotics
Coumarins (novobiocin, coumermycin A1)
inhibit bacterial Type II topoisomerases from binding ATP
Quinolones (nalidixic acid; ciproflaoxadin, Cipro)
inhibit the last step, which is resealing the DNA strand breaks
wide-spectrum and mostly selective for bacterial enzymes

66. Topoisomerase Inhibitors Used as Antibiotics
BOX 24-1 FIGURE 1 part 1

67. Topoisomerase Inhibitors Used as Chemotherapy Agents
Targets cancer because most rapidly growing cells (tumors, others) express topoisomerases
Eukaryotic Type I topoisomerase inhibitors
captothecin, irinotecan (Campto), topotecan (Hycamtin)
trap the enzyme-DNA complex in its cleaved state
Eukaryotic Type II topoisomerase inhibitors
doxorubicin (Adriamycin), etoposide (Etopophos), ellepticine

68. Topoisomerase Inhibitors Used as Chemotherapy Drugs
BOX 24-1 FIGURE 1 part 2

69. Supercoiled DNA Forms Plectonomic or Toroid/Solenoid Structures (or a Combination)
seen in plasmids
involves a right-hand superhelix with terminal loops
Toroid/solenoid
used in chromatin
involves tight left-hand turns
can resemble a garden hose on a reel
provides more compaction

70. Plectonemic Supercoiling
FIGURE 24–21 Plectonemic supercoiling. (a) Electron micrograph of plectonemically supercoiled plasmid DNA and (b) an interpretation of the observed structure. The purple lines show the axis of the supercoil; note the branching of the supercoil. (c) An idealized representation of this structure.

71. Plectonomic and Solenoidal Supercoiling
FIGURE 24–22 Plectonemic and solenoidal supercoiling of the same DNA molecule, drawn to scale. Plectonemic supercoiling takes the form of extended right-handed coils. Solenoidal negative supercoiling takes the form of tight left-handed turns about an imaginary tubelike structure. The two forms are readily interconverted, although the solenoidal form is generally not observed unless certain proteins are bound to the DNA. Solenoidal supercoiling provides a much greater degree of compaction.

72. Eukaryotic Chromosome Structure Changes over the Course of a Cell Cycle
Nondividing state (G0) and interphase (Gap1, G1; synthesis, S; and Gap2, G2):
Chromatin is amorphous and randomly dispersed.
Prophase of mitosis
Chromosomes become condensed, and pairs of sister chromatids form.

73. Changes in Chromosome Structure During the Cell Cycle
FIGURE 24–23 Changes in chromosome structure during the eukaryotic cell cycle. The relative lengths of the phases shown here are for convenience only. The duration of each phase varies with cell type and growth conditions (for single-celled organisms) or metabolic state (for multicellular organisms); mitosis is typically the shortest. Cellular DNA is uncondensed throughout interphase, as shown in the cartoons of thenucleus in the diagram. The interphase period can be divided (see Fig. 12–44) into the G1 (gap) phase; the S (synthesis) phase, when the DNA is replicated; and the G2 phase, throughout which the replicated chromosomes (chromatids) cohere to each another. Mitosis can be divided into four stages. The DNA undergoes condensation in prophase. During metaphase, the condensed chromosomes line up in pairs along the plane halfway between the spindle poles. The two chromosomes of each pair are linked to different spindle poles via microtubules that extend between the spindle and the centromere. The sister chromatids separate at anaphase, each drawn toward the spindle pole to which it is connected. The process is completed in telophase. After cell division is complete, the chromosomes decondense and the cycle begins anew.

74. DNA Packing into Chromatin
Chromatin consists of fibers of protein and DNA and a small amount of RNA.
DNA associates tightly with proteins called histones.
small proteins with lots of basic (Lys, Arg) residues
modified by methylation, acetylation, ADP-ribosylation, phosphorylation, glycosylation, sumoylation, ubiquination
DNA and protein are packed into discrete units called nucleosomes.

75. Nucleosomes
FIGURE 24–24 Nucleosomes. (a) Regularly spaced nucleosomes consist of core histone proteins bound to DNA. (b) In this electron micrograph, the DNA-wrapped histone octamer structures are clearly visible.

76. Nucleosomes Consist of DNA Wrapped Around Histones
DNA of length 105 m  fits into a nucleus of diameter 5–10 m.
Partial unfolding reveals “beads on a string.”
Beads are ~146 bp of DNA wrapped around eight histones (the “core”);there are two of each: H2A, H2B, H3, H4.
It forms a left-hand solenoid.
The string is a “linker” DNA of ~54 bp bound to histone H1.
Amino-terminal tails of histones stick out, form sites for covalent modification, and form important contacts between nucleosomes.

77. Types and Properties of the Common Histones
TABLE 24-5
Types and Properties of the Common Histones
Histones
Molecular weight
Number of amino acid residues
Content of basic amino acids (% of total)
Lys
Arg
H1a
21,130
223
29.5
11.3
H2Aa
13,960
129
10.9
19.3
H2Ba
13,774
125
16.0
16.4 H3
15,273
135
19.6
13.3 H4
11,236
102
10.8
13.7
aThe sizes of these histones vary somewhat from species to species. The numbers given here are for bovine histones.

78. DNA Wrapped Around a Histone Core
FIGURE 24–25a DNA wrapped around a histone core. (a) The simplified structure of a nucleosome octamer (left) with DNA wrapped around the histone core (right).

79. FIGURE 24–25b,c DNA wrapped around a histone core
FIGURE 24–25b,c DNA wrapped around a histone core. (b) A ribbon representation of the nucleosome from the African frog Xenopus laevis. Different colors represent the different histones, matching the colors in (a). (c) Surface representation of the nucleosome. The view in (c) is rotated relative to the view in (b) to match the orientation shown above in (a). A 146 bp segment of DNA in the form of a left-handed solenoidal supercoil wraps around the histone complex 1.67 times.

80. Front and Side Views of Histone Amino-Terminal Tails
FIGURE 24–25d DNA wrapped around a histone core. (d) Two views of histone amino-terminal tails protruding from between the two DNA duplexes that supercoil around the nucleosome. Some tails pass between the supercoils through holes formed by alignment of the minor grooves of adjacent helices. The H3 and H2B tails emerge between the two coils of DNA wrapped around the histone; the H4 and H2A tails emerge between adjacent histone subunits.

81. How Amino-Terminal Tails Interact Between Nucleosomes
FIGURE 24–25e DNA wrapped around a histone core. (e) The amino-terminal tails of one nucleosome extrude from the particle and interact with adjacent nucleosomes, helping to define higher-order DNA packaging.

82. Nucleosomal DNA Is Underwound
Wrapping DNA around the histone core requires removal of one helical turn.
The underwinding occurs without a strand break, so a compensatory (+) supercoil forms.
This (+) supercoil is relaxed by a topoisomerase, leaving DNA with net negative supercoil.

83. Histone Binding Depends on DNA Sequence
Histone binding is not random.
It occurs more often at A-T–rich regions.
Staggering AA, AT, or TT at 10 bp intervals (phased with pitch of helix) narrows the minor groove and bends the DNA.
 facilitates its binding around the histone core

84. Effect of DNA Sequence on Nucleosome Binding
FIGURE 24–27 The effect of DNA sequence on nucleosome binding. (PDB ID 1AOI) Runs of two or more A=T base pairs facilitate the bending of DNA, while runs of two or more G≡C base pairs have the opposite effect. When spaced at about 10 bp intervals, consecutive A=T base pairs help bend DNA into a circle. When consecutive G≡C base pairs are spaced 10 bp apart, and offset by 5 bp from runs of A=T base pairs, DNA binding to the chromosome is facilitated.

85. Nucleosomes Then Assemble into Higher-Order Structures
Nucleosome formation compacts DNA seven-fold…but overall compaction is >10K-fold!
Next level of structure: 30 nm fiber
It occurs in regions where sequence-specific, non-histone proteins bind (known as a territory).
Chromosomes with large amounts of heterochromatin are typically found at the nuclear periphery.

86. The 30 nm Fiber
FIGURE 24–28 Higher-order organization of nucleosomes. The compact fiber is formed by the tight packing of nucleosomes. (a) The 30 nm fiber, as seen by electron microscopy. (b) A model for nucleosome organization within a 30 nm fiber. Two 10 nm fibers are coiled around each other, with nucleosomes stacked in each. DNA is blue; nucleosomes are yellow. (c) A crumpled globule folding arrangement of 10 nm fibers in a condensed chromosome. The folding appears to be random, but nearby chromosomal segments remain associated and the folding occurs so as to minimize the formation of knots.

87. Higher-Level Structures Depend on Chromosomal Scaffold
Higher-order structures are not well understood.
May vary between chromosomes, regions, and even moment of time.
Appears to involve a loop of DNA (maybe with related genes) associating with a scaffold of proteins
includes Topo II and SMC proteins
SMC = Structural Maintenance of Chromosomes

88. Loops of DNA Attached to a Chromosomal Scaffold
FIGURE 24–29 Loops of DNA attached to a chromosomal scaffold. (a) A swollen chromosome, produced in a buffer of low ionic strength, as seen in the electron microscope. Notice the appearance of 30 nm fibers (chromatin loops) at the margins. (b) Extraction of the histones leaves a proteinaceous chromosomal scaffold surrounded by naked DNA. (c) The DNA appears to be organized in loops attached at their base to the scaffold in the upper left corner. Scale bar = 1 µm. The three images are at different magnifications.

89. Condensed Chromosome Structure Is Maintained by SMC Proteins
SMC proteins have five domains.
N and C domains form an ATP-binding site.
Two major types:
cohesins – help link sister chromatids
condensins – help chromosomes to condense; create positive supercoils
See Figure

90. Structure of SMC Proteins
FIGURE 24–31 Structure of SMC proteins. (a) SMC proteins have five domains. (b) Each SMC polypeptide is folded so that the two coiled-coil domains wrap around each other and the N and C domains come together to form a complete ATP-binding site. Two polypeptides are linked at the hinge region to form the dimeric V-shaped SMC molecule. (c) Bacterial SMC proteins form a homodimer. The six different eukaryotic SMC proteins form heterodimers. Cohesins are made up of SMC1-SMC3 pairs, and condensins consist of SMC2-SMC4 pairs. The SMC5-SMC6 pair is involved in DNA repair. (d) Electron micrographs of SMC dimers from the bacterium Bacillus subtilis.

91. Bacterial DNA Is Organized into Nucleoids
It can occupy much of the cell volume.
DNA attaches to the plasma membrane.
A scaffold-like structure organizes the circular DNA into ~500 looped domains
DNA binds to proteins transiently.
example: protein HU

92. Possible Role of Condensins
FIGURE 24–32 The possible role of condensins in chromatin condensation. Initially, the DNA is bound at the hinge region of the SMC protein, in the interior of what can become an intramolecular SMC ring. ATP binding leads to head-to-head association, forming supercoiled loops in the bound DNA. Subsequent rearrangement of the head-to-head interactions to form rosettes condenses the DNA. Condensins may organize the looping of the chromosome segments in a number of ways. Two current models are shown.

93. Roles of Cohesins and Condensins in the Cell Cycle
FIGURE 24–33 The roles of cohesins and condensins in the eukaryotic cell cycle. Cohesins are loaded onto the chromosomes during G1 (see Fig. 24–24), tying the sister chromatids together during replication. At the onset of mitosis, condensins bind and maintain the chromatids in a condensed state. During anaphase, the enzyme separase removes the cohesin links. Once the chromatids separate, condensins begin to unload and the daughter chromosomes return to the uncondensed state.

94. E. Coli Nucleoids
FIGURE 24–34 E. coli nucleoids. The DNA of these cells is stained with a dye that fluoresces blue when exposed to UV light. The blue areas define the nucleoids. Notice that some cells have replicated their DNA but have not yet undergone cell division and hence have multiple nucleoids.

95. Looped Domains of the E. Coli Chromosome
FIGURE 24–35 Looped domains of the E. coli chromosome. Each domain is about 10,000 bp in length. The domains are not static, but move along the DNA as replication proceeds. Barriers at the boundaries of the domains, of unknown composition, prevent the relaxation of DNA beyond the boundaries of the domain where a strand break occurs. The putative boundary complexes are shown as gray-shaded ovoids. The arrows denote movement of DNA through the boundary complexes.

96. Chapter 24: Summary In this chapter, we learned that:
genetic information of the cell is encoded in the nucleotide sequence of one or several DNA molecules
the protein-coding regions represent only a small fraction of the total DNA
telomeres and centromeres regulate cell division
bacterial DNA is usually supercoiled for efficient packing
eukaryotic DNA is wound around positively charged histones
higher-order organization of chromatin likely involves coils upon coils upon coils