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H2O, or H2) of each atom in alanine generated in the Miller- Urey experiment.
2.Following the populations. In an experiment analogous to the Spiegelman experiment, suppose that a population of RNA molecules consists of 9 identical molecules, each of which replicates once in 15 minutes, and 1 molecule that replicates once in 5 minutes. Estimate the composition of the population after 1, 10, and 25 “generations” if a generation is defined as 15 minutes of replication. Assume that all necessary components are readily available.
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3.Selective advantage. Suppose that a replicating RNA molecule has a mutation (genotypic change) and the phenotypic result is that it binds nucleotide monomers more tightly than do other RNA molecules in its population. What might the selective advantage of this mutation be? Under what conditions would you expect this selective advantage to be most important?
4.Opposite of randomness. Ion gradients prevent osmotic crises, but they require energy to be produced. Why does the formation of a gradient require an energy input?
5.Coupled gradients. How could a proton gradient with a higher concentration of protons inside a cell be used to pump ions out of a cell?
6.Proton counting. Consider the reactions that take place across a photosynthetic membrane. On one side of the membrane, the following reaction takes place:
whereas, on the other side of the membrane, the reaction is:
How many protons are made available to drive ATP synthesis for each reaction cycle?
7.An alternative pathway. To respond to the availability of sugars such as arabinose, a cell must have at least two types of proteins: a transport protein to allow the arabinose to enter the cell and a gene-control protein, which binds the arabinose and modifies gene expression. To respond to the availability of some very hydrophobic molecules, a cell requires only one protein. Which one and why?
8.How many divisions?In the development pathway of C. elegans,cell division is initially synchronous—that is, all cells divide at the same rate. Later in development, some cells divide more frequently than do others. How many times does each cell divide in the synchronous period? Refer to Figure 2.26.
40CHAPTER 2 •Biochemical Evolution
Need extra help?Purchase chapters of the Student Companionwith complete solutions online at w.whfreeman.com/ biochem5.
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CHAPTER 3 Protein Structure and Function
Proteinsare the most versatile macromolecules in living systems and serve crucial functions in essentially all biological processes. They function as catalysts, they transport and store other molecules such as oxygen, they provide mechanical support and immune protection, they generate movement, they transmit nerve impulses, and they control growth and differentiation. Indeed, much of this text will focus on understanding what proteins do and how they perform these functions.
Several key properties enable proteins to participate in such a wide range of functions.
1.Proteins are linear polymers built of monomer units called amino acids. The construction of a vast array of macromolecules from a limited number of monomer building blocks is a recurring theme in biochemistry. Does protein function depend on the linear sequence of amino acids? The function of a protein is directly dependent on its threedimensional structure (Figure 3.1). Remarkably, proteins spontaneously fold up into three-dimensional structures that are determined by the sequence of amino acids in the protein polymer. Thus, proteins are the embodiment of the transition from the one-dimensional world of sequences to the three-dimensional world of molecules capable of diverse activities.
2.Proteins contain a wide range of functional groups. These functional groups include alcohols, thiols, thioethers, carboxylic
3.1ProteinsAre Built from a Repertoire of 20 Amino Acids
3.2PrimaryStructure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains
3.3 Secondary Structure: Polypeptide Chains Can Fold into Regular Structures Such as the Alpha Helix, the Beta Sheet, and Turns and Loops
3.4 Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures with Nonpolar Cores
3.5 Quaternary Structure: Polypeptide Chains Can Assemble into Multisubunit Structures
3.6TheAmino Acid Sequence of a Protein Determines Its Three- Dimensional Structure
Crystals of human insulin. Insulin is a protein hormone, crucial for maintaining blood sugar at appropriate levels. (Below) Chains of amino acids in a specific sequence (the primary structure) define a protein like insulin. These chains fold into well-defined structures (the tertiary structure)—in this case a single insulin molecule. Such structures assemble with other chains to form arrays such as the complex of six insulin molecules shown at the far right (the quarternary structure). These arrays can often be induced to form well-defined crystals (photo at left), which allows determination of these structures in detail. [(Left) Alfred Pasieka/Peter Arnold.]
Leu Tyr Gln
Leu Glu Asn
Primarystructure Secondarystructure Tertiarystructure
7552dc03_41-76 4/17/01 7:2 AM Page 41 acids, carboxamides, and a variety of basic groups. When combined in various sequences, this array of functional groups accounts for the broad spectrum of protein function. For instance, the chemical reactivity associated with these groups is essential to the function of enzymes,the proteins that catalyze specific chemical reactions in biological systems (see Chapters 8–10).
3.Proteins can interact with one another and with other biological macromolecules to form complex assemblies. The proteins within these assemblies can act synergistically to generate capabilities not afforded by the individual component proteins (Figure 3.2). These assemblies include macromolecular machines that carry out the accurate replication of DNA, the transmission of signals within cells, and many other essential processes.
4.Some proteins are quite rigid, whereas others display limited flexibility. Rigid units can function as structural elements in the cytoskeleton (the internal scaffolding within cells) or in connective tissue. Parts of proteins with limited flexibility may act as hinges, springs, and levers that are crucial to protein function, to the assembly of proteins with one another and with other molecules into complex units, and to the transmission of information within and between cells (Figure 3.3).
FIGURE 3.2A complex protein assembly.An electron micrograph of insect flight tissue in cross section shows a hexagonal array of two kinds of protein filaments. [Courtesy of Dr. Michael Reedy.]
42 CHAPTER 3 •Protein Structure and Function
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