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Chapter 4 : An Overview of Molecular Biology

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An Overview of Molecular Biology, Page 1 of 2

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Abstract:

This chapter states that the forms and functions of proteins are central to molecular biology. The mechanism of RNAi is described in more detail. A central theme of gene regulation is that it involves interactions between proteins and other molecules: additional proteins, small molecules, RNA, and DNA. These interactions are dependent (as are all protein functions) upon the three-dimensional structures of the proteins. The chapter talks about protein structure and function, and looks closely at the structures of two DNA-binding regulatory proteins and how they interact with DNA. Genes are important because they supply information that directs the synthesis of proteins. It is the proteins that confer a phenotype on the cell: its biochemical capabilities, its shape, its communication channels, and so on. The chapter focuses on the effects of mutations in terms of how specific nucleic acid changes affect protein structure and function, and on some specific effects of amino acid changes on proteins. It emphasizes that all the cellular operations involving DNA are performed by enzymes.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4

Key Concept Ranking

Gene Expression and Regulation
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Immune System Proteins
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Tobacco mosaic virus
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Aromatic Amino Acids
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Figures

Image of Figure 4.1
Figure 4.1

The nucleotide. Carbon atoms of the deoxyribose sugar portion are numbered according to chemical convention.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.2
Figure 4.2

A trinucleotide.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.3
Figure 4.3

Complementary base pairs in DNA.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.4
Figure 4.4

Ribbon model of DNA.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.5
Figure 4.5

DNA replication. (A) Base pairing between an incoming nucleotide and the template strand of DNA guides the formation of a new daughter strand with a complementary base sequence. (B) In each round of DNA replication, each of the two DNA strands is used as a template for the synthesis of a new complementary strand, resulting in two daughter molecules, each with one “new” and one “old” strand.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.6
Figure 4.6

A protein is a chain of amino acids (represented by beads) that folds into a specific three-dimensional shape. The three-letter abbreviations on the beads are standard for specific amino acids (see Figure 4.23 ).

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.7
Figure 4.7

The base sequence of DNA determines the amino acid sequence of proteins.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.8
Figure 4.8

Chemical differences between DNA and RNA.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.9
Figure 4.9

A single-stranded RNA molecule.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.10
Figure 4.10

Transcription.(A) Base pairing between an incoming ribonucleotide and the DNA template guides the formation of a complementary mRNA molecule. The DNA template closes behind the RNA synthesis site, releasing the new RNA molecule.(B) In transcription, a single DNA strand is used as a template. The RNA transcript is released, leaving the DNA molecule intact.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.11
Figure 4.11

A tRNA molecule. Complementary base pairing between different portions of the tRNA molecule maintains its shape.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.12
Figure 4.12

Translation. Complementary base pairing between the anticodons of incoming tRNA molecules and the codons of the mRNA guides the formation of the amino acid chain.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.13
Figure 4.13

Major genetic traffic signals in bacteria. These signals tell RNA polymerase where to begin and end transcription, enable the ribosome to recognize mRNA, and direct the ribosome to start and stop protein synthesis. RRE, ribosome recognition element.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.14
Figure 4.14

Splicing of precursor RNA to create mRNA.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.15
Figure 4.15

Transcriptional regulation of the operon. P is the promoter; O is the operator.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.16
Figure 4.16

Transcriptional regulation of the operon. P is the promoter; O is the operator.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.17
Figure 4.17

Activator proteins are needed for transcription in eukaryotic cells.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.18
Figure 4.18

osmotically shocked to release DNA. (Photograph copyright K.G.Murti/Visuals Unlimited.)

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.19
Figure 4.19

Electron micrographs of various viruses. (A) Bacteriophage lambda (magnification, ×275,000). (Photograph copyright K. G. Murti/Visuals Unlimited.) (B) Purified bacteriophage T4. (Photograph courtesy of F. P. Booy; reprinted from J. D. Karam et al., ed., , ASM Press, Washington, DC, 1994.) (C) Tobacco mosaic virus (magnification, ×144,000). (Photograph copyright K. G. Murti/ Visuals Unlimited.) (D) Vesicular stomatitis virus (rabies group) (magnification, ×100,000). (Photograph copyright K. G. Murti/Visuals Unlimited.)

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.20
Figure 4.20

General structure of an amino acid. R signifies one of the 20 different side chains shown in Figure 4.23 .

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.21
Figure 4.21

To form proteins, amino acids are joined by peptide bonds.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.22
Figure 4.22

A polar covalent bond. Although the oxygen and hydrogen nuclei are sharing two electrons, the highly electronegative oxygen nucleus tends to draw them away from the weakly electronegative hydrogen nucleus. As a result, the oxygen end of the bond acquires a partial negative charge, while the hydrogen end is partially positive.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.23
Figure 4.23

The amino acids commonly found in proteins. The three-letter abbreviation for each amino acid is shown beneath its full name.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.24
Figure 4.24

Water is a very polar molecule. The strongly electronegative oxygen nucleus hogs the electrons it shares with the hydrogen nuclei.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.25
Figure 4.25

A hydrogen bond (dotted line) is a weak electrostatic attraction between opposite partial charges.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.26
Figure 4.26

Common hydrogen bonds in biological systems.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.27
Figure 4.27

The alpha helix. C indicates the carbon atoms with side chains, which are not shown.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.28
Figure 4.28

A beta sheet. C indicates the carbon atoms with side chains, which are not shown.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.29
Figure 4.29

In this drawing of the replication termination protein of , each sphere represents an atom. Even though this protein is small, its structure is complex.(Drawing courtesy of Stephen White, in whose laboratory the structure was determined.)

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.30
Figure 4.30

Ribbon drawings of protein structures. The beta strands in panels A and B are numbered in order from the N terminus to the C terminus of the amino acid chain. (Drawings courtesy of Jane Richardson.)

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.31
Figure 4.31

Some protein structure motifs. (Panels A and C are from C. Branden and J. Tooze, Introduction to Protein Structure, Garland Publishing, Inc., New York, NY, 1991; panels B and D are from A. Lehninger, D. Nelson, and M. Cox, Principles of Biochemistry, 2nd ed., Worth Publishers, Inc., New York, NY, 1993.)

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.32
Figure 4.32

Domain structure of the bacteriophage lambda repressor protein. (A) The N-terminal domain consists of amino acids 1 through 92, and the C terminal domain consists of residues 132 through 236. (B) The repressor forms dimers through the interaction of the C-terminal domains. The N-terminal domains bind to a specific DNA sequence. (From M. Ptashne, , 3rd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2004.)

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.33
Figure 4.33

Disulfide bridges stabilize protein structure. (Panel B is from C. Branden and J. Tooze, Introduction to Protein Structure, Garland Publishing, Inc., New York, NY, 1991.)

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.34
Figure 4.34

Domain structures of some modular proteins. Epidermal growth factor (EGF) is a protein that signals several cell types to divide. The other four proteins are protein-cleaving enzymes with a variety of physiological roles. (From C. Branden and J. Tooze, , Garland Publishing, Inc., New York, NY, 1991.)

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.35
Figure 4.35

Keratin, a structural protein. (A) A single keratin molecule forms a long alpha helix. (B) Two keratin alpha helices then wrap around each other. (From J. D. Watson et al., , 4th ed., vol. 1, Benjamin/Cummings, Menlo Park, CA, 1987. Reprinted by permission of Addison Wesley Longman Publishers, Inc.) (C) Two-chain coils lie end to end and side by side, forming fibers. (From A. Lehninger, D. Nelson, and M. Cox, , 2nd ed., Worth Publishers, Inc., New York, NY, 1993.)

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.36
Figure 4.36

The biochemistry of a permanent hair wave.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.37
Figure 4.37

Binding of lambda repressor protein to DNA. (From M. Ptashne, A Genetic Switch, 3rd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2004.)

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.38
Figure 4.38

Binding of the amino acid tryptophan to the trp repressor protein changes the conformation of the repressor so that it can bind to DNA. (Reprinted by permission from Nature 327:591–597, 1987.)

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.39
Figure 4.39

Mechanism of action of the proteinase chymotrypsin, an example of a serine protease. (Panel D is from C. Branden and J. Tooze, Introduction to Protein Structure, Garland Publishing, Inc., New York, NY, 1991.)

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.40
Figure 4.40

Representation of sickle-cell hemoglobin aggregation. (A) Normal hemoglobin molecules do not stick together. (B) The hydrophobic patch on the surface of sickle-cell hemoglobin caused by the glutamateto-valine substitution at position 6 (Val-6) fits neatly into a hydrophobic pocket on a second molecule. Thus, sickle-cell hemoglobin molecules can polymerize in a head-to-tail fashion.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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Image of Figure 4.41
Figure 4.41

Schematic representation of how the loss of 70 C-terminal amino acids from a receptor protein results in increased red blood cell (RBC) production.

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4
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References

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1. Bayley, H. 1997. Building doors into cells. Scientific American277:62. Examples of protein engineering projects.
2. Branden, C.,, and J. Tooze. 1991. Introduction to Protein Structure. Garland Publishing, Inc., New York, NY. Well-illustrated, readable book about protein structure.
3. Cuerces-Amabile, C.,, and M. Chicurel. 1993. Horizontal gene transfer. American Scientist 81:332341. Transfer of genetic information outside of parent to offspring.
4. Doolittle, R.,, and P. Bork. 1993. Evolutionarily mobile modules in proteins. Scientific American 269:5056. Protein domain structure.
5. Gerstein, M.,, and M. Levitt. 1998. Simulating water and the molecules of life. Scientific American 279:100.
6. Gibbs, W. 2003. The unseen genome: gems among the junk. Scientific American 289:2633.
7. Hall, S. 1995. Protein images update natural history. Science 267:620624. How protein structure determinations and new computer models of protein structure are changing the science of biology.
8. Holtzman, D. 1991. A “jumping gene” caught in the act. Science 254:17281729. Two cases of human hemophilia A apparently caused by the movement of a transposon.
9. Kreuzer, H.,, and A. Massey. 2006. Biology and Biotechnology: Science, Applications, and Issues. ASM Press, Washington, DC. A discussion of biotechnology in the context of the biology of cells. Approximately half the book is devoted to an overview of cell biology. The other half presents detailed discussions of applications of biotechnology in agriculture, medicine, food, and nutrition, with emphasis on the role of public policy in the development of science.
10. McGinnis, W.,, and M. Kuziora. 1994. The molecular architects of body design. Scientific American 270:5866. Genes, proteins, and development.
11. Micklos, D.,, and G. Freyer. 2003. DNA Science, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
12. Moxon, E. R.,, and C. Wills. 1999. DNA microsatellites: agents of evolution? Scientific American 280:94.
13. Prusiner, S. 1995. The prion diseases. Scientific American 272:48.
14.
15. Ptashne, M. 1989. How gene activators work. Scientific American 260:40–47.
16.
17. Ptashne, M. 2004. A Genetic Switch, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. Excellent short book describing in molecular detail how bacteriophage lambda switches from lysogenic to lytic growth. Protein structure, protein-protein interactions, protein-DNA interactions, and gene regulation are combined in one well-understood biological system.
18.
19. Rennie, J. 1993. DNA's new twists. Scientific American 266:122132. Current thinking about DNA structure.
20.
21. Rhodes, D.,, and A. Klug. 1993. Zinc fingers. Scientific American 268:5665. Protein structure and gene regulation; zinc fingers are one structural motif used for DNA binding.
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23. Richards, F. 1991. The protein folding problem. Scientific American 264:5463. An overview of the attempt to understand what determines three-dimensional protein structure.
24.
25. Roush, W. 1995. An “off switch” for red blood cells. Science 268:2728. Description of the molecular biology of the stamina- enhancing mutation causing benign erythrocytosis.
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27. Stix, G. 2004. Hitting the genetic off switch. Scientific American 291:98101.
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29. Tjian, R. 1995. Molecular machines that control genes. Scientific American 272:5461. Description of the complex assembly of proteins needed for transcription of eukaryotic genes.
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31. Wallace, D. 1997. Mitochondrial DNA in aging and disease. Scientific American 277:40.
32. Zamore, D. Z. 2002. Ancient pathways programmed by small RNAs. Science 296:12651269.

Tables

Generic image for table
Table 4.1

The genetic code

Citation: Kreuzer H, Massey A. 2008. An Overview of Molecular Biology, p 97-136. In Molecular Biology and Biotechnology: A Guide for Teachers, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816100.ch4

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