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Chapter 5 : Protein Structure and Function

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Protein Structure and Function, Page 1 of 2

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Abstract:

This chapter focuses on the structure of proteins and how it relates to their functions. When a protein folds, it generally segregates the hydrophobic side chains in the interior of the protein, where they interact with one another away from water molecules in the cytoplasm. Protein structure is held together by hydrogen bonds and disulfide bridges between cysteine residues. Proteins can be denatured by treatments that break these bonds, such as heat or harsh chemicals. If a protein is denatured, it often cannot refold itself even if the denaturing agent is removed. Proteins carry out functions through molecular interactions between specific side chains and their targets. Scientists also learn about new proteins by comparing their amino acid sequences to the sequences of all other known proteins, using national databases and search engines. Researchers are using their knowledge of protein structure and protein function to improve the usefulness of enzymes in industrial and other processes. They do this by manipulating the DNA sequences of genes encoding these proteins, so that the proteins can have altered amino acid sequences and characteristics.

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Figures

Image of Figure 5.1
Figure 5.1

General structure of an amino acid. R signifies one of the 20 different side chains shown in Figure 5.4 .

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.2
Figure 5.2

Peptide bonds. Peptide bonds are formed between the NH group of one amino acid and the COOH group of another, with the formation and loss of a water molecule. R, amino acid side chain. A protein has a polypeptide backbone with various amino acid side chains.

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.3
Figure 5.3

A polar chemical bond. Although the oxygen and hydrogen nuclei share 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. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.4
Figure 5.4

Amino acids commonly found in proteins.

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.5
Figure 5.5

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. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.6
Figure 5.6

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

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.7
Figure 5.7

Common hydrogen bonds (dotted lines) in biological systems.

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.8
Figure 5.8

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

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.9
Figure 5.9

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

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.10
Figure 5.10

Two cysteine side chains can form a disulfide bridge.

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.11
Figure 5.11

A ball-and-stick representation of the protein flavodoxin. (Image courtesy of Antonio Romero and Javier Sancho.)

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.12
Figure 5.12

Ribbon drawings of protein structures. (Drawings courtesy of Jane Richardson.)

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.13
Figure 5.13

Domain structure of the bacteriophage lambda repressor protein. The N-terminal domain consists of amino acids 1 to 92, and the C-terminal domain consists of amino acids 132 to 236. The repressor forms dimers through interactions between the C-terminal domains. The N-terminal domains bind to a specific DNA base sequence. (From M. Ptashne, , 2nd ed. [Blackwell Scientific Publishing and Cell Press, Cambridge, Mass., 1992].)

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.14
Figure 5.14

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-digesting enzymes with a variety of physiological roles.

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.15
Figure 5.15

Keratin, a structural protein. The keratin polypeptide forms an alpha helix with hydrophobic side chains (not shown). Two keratin helices wrap tightly around one another. The coiled helices lie side by side and end to end, forming fibers.

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.16
Figure 5.16

Biochemistry of a permanent hair wave.

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.17
Figure 5.17

Binding of lambda repressor protein to DNA. (From M. Ptashne, , 2nd ed. [Blackwell Scientific Publishing and Cell Press, Cambridge, Mass., 1992].)

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.18
Figure 5.18

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 from 591–597, 1987, with permission.)

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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Image of Figure 5.19
Figure 5.19

Protein stability engineering. Three engineered disulfide bridges (gold) tie the two domains of bacteriophage T4 lysozyme in the proper configuration. The two domains are shown in lavender and green. The numbers indicate the positions of the cysteines in the 164-amino-acid polypeptide. The cysteine at position 54 was changed to a threonine to keep it from interfering with proper formation of the engineered bridges. (Adapted from M. Matsumara, G. Signor, and B.W. Matthews, 291, 1989, with permission.)

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5
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References

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Tables

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Table 5.1

Levels of protein structure

Citation: Kreuzer H, Massey A. 2005. Protein Structure and Function, p 89-110. In Biology and Biotechnology. ASM Press, Washington, DC. doi: 10.1128/9781555816094.ch5

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