Chapter 2

Nucleic Acids

George Plopper

Figure 02.01: Some forms of information storage in cells.

Figure 02.02: Mistakes in DNA replication may cause mutations.

Figure 02.03: DNA information is "read" by proteins.

Figure 02.04: The smallest function unit of DNA is a gene.

Figure 02.05: An overview of translation in eukaryotes.

Figure 02.06: Mutations can alter amino acid sequence and protein function.

Figure 02.07: A single point mutation causes sickle cell disease.

Figure 02.08: Mutations accumulate slowly in a population of cells.

Table 02.T01: A comparison of properties for three forms of information storage.

George Plopper

Figure 02.09A: A step-wise method for drawing a deoxyribonucleotide.

Figure 02.09B: A step-wise method for drawing a deoxyribonucleotide.

Figure 02.09C: A step-wise method for drawing a deoxyribonucleotide.

Figure 02.10: Distinctinctive features of ribonucleotides.

Figure 02.11: The general structure of a nucleic acid.

Figure 02.12A: Level 1 of DNA organization is a double stranded, antiparallel double helix held together by hydrogen bonds between base pairs.

Figure 02.12B: A 3D drawing showing the spatial arrangement of the nucleotides in a DNA double helix.

Figure 02.12C: A space-filling model of the DNA double helix (B form), indicating the location and size of the major and minor grooves.

© Photodisc

Figure 02.13: Three different forms of double helical DNA (L to R: A form, B form, Z form). Note that all three forms have major and minor grooves.

Courtesy of Richard Wheeler

iClicker timeWhich statement about carbon is false? A. It can form covalent bonds with four different atoms.B. It can form hydrogen bonds with water.C. It can form covalent bonds with other carbon atoms.D. It can form covalent bonds with oxygen.E. It can form covalent bonds with nitrogen.

Learning Outcomes, Monday 1/30

• Define a nucleosome and explain its significance in DNA organization.

• Distinguish between euchromatin and heterochromatin in an electron micrograph, and explain the functional difference between them.

• Define the nuclear pore complex and explain its role in protecting DNA

Figure 02.BF01: The Library of Congress analogy for information storage and transmission in cells.

© iStockphoto/Thinkstock

Figure 02.14_BTM: A computer model of DNA wrapped around core particle.

Photos courtesy of E. N. Moudrianakis, John Hopkins University.

Figure 02.14_TOP: Octameric arrangement of histones in core particle, with DNA wrapped around it. Histone H1 pins the DNA to the core particle.

Figure 02.15A: The 30-40 nm fiber is made by coiling the "beads-on-a-string" arrangement of nucleosomes. EMs show evidence for both forms in isolated

chromatin.

Courtesy of Ada L. Olins and Donald E. Olins, Bowdoin College.

Figure 02.15B: The 30-40 nm fiber is made by coiling the "beads-on-a-string" arrangement of nucleosomes. EMs show evidence for both forms in isolated

chromatin.

Courtesy of Ada L. Olins and Donald E. Olins, Bowdoin College.

Figure 02.15C: The 30-40 nm fiber is made by coiling the "beads-on-a-string" arrangement of nucleosomes. EMs show evidence for both forms in isolated

chromatin.© Dr. Donald Fawcett, H. Ris/Visuals Unlimited, Inc.

Figure 02.16: SWI/SNF proteins participate in chromatin remodeling by partially unwrapping DNA around nucleosomes, allowing them to slide the core particle.

Figure 02.17A: Chemical modification of histone tails changes the shape of nucleosomes. A. The exact shape of the tail regions of the histones is not known, but

they are long enough to project out of the core particle.

Figure 02.17B: Chemical modification of histone tails changes the shape of nucleosomes. B.The tail regions likely project past the DNA double helix, and are

flexible.

Figure 02.17C: Chemical modification of histone tails changes the shape of nucleosomes. C. When methyl, acetyl, or phosphate groups are attched to the tails,

the tails change shape, altering access to the DNA wrapped around the core particle. In most cases, these modifications restrict access to the underlying DNA. The actual

shape of the modified tails is now known.

Figure 02.18: Methylated bases found in DNA. The methyl groups are indicated in [color].

Figure 02.19: Level 4 of DNA organization can be seen in this electron micrograph of loop domains projecting outward from the protein/RNA scaffold.

Reproduced from Cell, vol. 12, Paulson, J. R., and Laemmli, U. K., The structure of histone..., pp. 817-828. Copyright 1977, with permission from Elsevier. Photo courtesy of Ulrich K. Laemmli, University of Geneva, Switzerland.

Figure 02.20A: Chromosomes at different levels of DNA compaction.

© Dr. Robert Calentine/Visuals Unlimited, Inc.

Figure 02.21A: The five different levels of DNA organization in eukaryotic cells.

Figure 02.21B: The five different levels of DNA organization in eukaryotic cells.

Figure 02.21C: The five different levels of DNA organization in eukaryotic cells.

Figure 02.21D: The five different levels of DNA organization in eukaryotic cells.

Figure 02.21E: The five different levels of DNA organization in eukaryotic cells.

Figure 02.21A_INS: The five different levels of DNA organization in eukaryotic cells. Note that two types of level 5 (heterochromatin) are shown: 5A is found in non-dividing (interphase) cells, and 5B is found only in cells undergoing cell division

(mitosis or meiosis).

© Science Source/Photo Researchers, Inc.

Figure 02.21B_INS: The five different levels of DNA organization in eukaryotic cells.

© Donald Fawcett/Visuals Unlimited, Inc.

Figure 02.21C_INS: The five different levels of DNA organization in eukaryotic cells.

Reproduced from D. von Wettstein. 1971. Proc. Natl. Acad. Sci. USA. 68: 851-855. Courtesy of D. von Wettstein, Washington State University.

Figure 02.21D_INS: The five different levels of DNA organization in eukaryotic cells.

Courtesy of Bruno Zimm and Ruth Kavenoff.

Figure 02.21E_INS: The five different levels of DNA organization in eukaryotic cells.

Used with permission of Georgianna Zimm, University of California, San Diego. Courtesy of the Cell Image Library.

Figure 02.22: Heterochromatin appears as dark patches in the nucleus during interphase. This is Level 5A of DNA organization.

Photo courtesy of Edmund Puvion, Centre National de la Recherche Scientifique.

Figure 02.23A: Histone modification can silence DNA to form heterochromatin.

Figure 02.23B: Histone modification can silence DNA to form heterochromatin.

Figure 02.24: Rpa1, Sir3, and Sir4 can silence DNA to form heterochromatin.

iClicker timeWhich statement best explains what the line in the picture at right is pointing to?

A. The line is pointing to ribosomes translating an mRNA molecule.B. The line is pointing to nucleosomes that form along a double stranded DNA molecule.C. The line is pointing to individual tubulin proteins in a microtubule.D. The line is pointing to the head group on a single phospholipid.E. The line is pointing to a globular domain in heterochromatin.

Figure 02.25A: Overview of the nucleus.

Figure 02.25B: Nuclear pore complexes are channels that penetrate the inner and outer nuclear membrane and regulate the traffic into and out of the nucleus.

Photo courtesy of Terry Allen, University of Manchester.

Figure 02.25C: Overview of the nucleus.

Figure 02.26A: The nuclear lamina form a fibrous network attached to the inner nuclear membrane. These fibers lie between nuclear pore complexes, as shown.

Figure 02.26B: The nuclear lamina form a fibrous network attached to the inner nuclear membrane. These fibers lie between nuclear pore complexes, as shown.

Reprinted from J. Struct. Biol., vol. 140, B. Fahrenkrog, et al., Domain-specific antibodies reveal multiple-site topology..., pp. 254-267, Copyright (2002) with permission from Elsevier [http://www.sciencedirect.com/science/journal/10478477]. Photos courtesy Ueli Aebi, University of Basel.

Figure 02.26C: The nuclear lamina form a fibrous network attached to the inner nuclear membrane. These fibers lie between nuclear pore complexes, as shown.

Main photo courtesy of Terry Allen, University of Manchester.

Learning Outcomes, Monday 1/30

• Define a nucleosome and explain its significance in DNA organization.

• Distinguish between euchromatin and heterochromatin in an electron micrograph, and explain the functional difference between them.

• Define the nuclear pore complex and explain its role in protecting DNA

Table 02.T02: The Bases, Nucleosides, and Nucleotides of RNA and DNA

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