Next page proteins

The amino acids, basic building blocks of proteins, all share this dual acid-base character. See Chapter 13 for a description of the amino acids and their biological chemistry. Organic bases also have a long and varied history as painkillers and narcotics, as our Chemishy and Life Box on the next page describes. 

There s not just one DNA polymerase there s a whole army. DNA replication actually occurs in large complexes containing many proteins and sometimes many polymerases. In eukaryotic cells we have to replicate both mitochondrial and nuclear DNA, and there are specific DNA polymerases for each. In addition to DNA replication, you have to make new DNA when you repair. Consequently, the function may be specialized for repair or replication. There can also be specialization for making the leading or lagging strand. Some of the activities of DNA polymerases from eukaryotes and prokaryotes are shown in the table on the next page. 

DNA is one type of nucleic acid. The other type of nucleic acid is called RNA (short for ribonucleic acid). RNA is present throughout a cell. It works closely with DNA to produce the proteins in the body. Table 2.3, on the next page, shows the structures of RNA and DNA. 

Yeast cells can exist as haploids of opposite mating types (either a or a). When an a and an a cell are allowed to mate, they form a diploid cell (a/a). To study interactions between two proteins, cDNA sequences of a protein of interest (PT1) are expressed as a fusion protein, linked to a DNA-binding domain (DBD) of a yeast gene-transcript activator in a haploid cell (e.g., a). cDNA sequences corresponding to another test protein (PT2) are linked to the Continued on next page)... 

Steps in prokaryotic protein synthesis (translation). (Continued on the next page)... 

Protein purification problem. Complete the table at the top of the next page. 

Several different plants have been used for the expression of proteins in plants. All these systems have certain advantages regarding edibility, growth rate, scalability, gene-to-protein time, yield, downstream processing, ease of use, and so on, which I will not discuss in further detail here. A selection of different expression systems is listed on the next page ... 

Desorption was much more rapid on HEMA than on EMA, indicating that weaker surface-protein interactions occur at more hydrophilic surfaces. Continued on next page... 

Amides are named by denoting the amine portion with N- and replacing -oic acid from the parent carboxylic acid with -amide. In the amide produced in the preceding reaction, the ethyl group comes from the amine, and the acid portion comes from ethanoic acid (acetic acid). Some amides are shown in Figure 15.17 on the next page. The most important example of the amide group is the peptide bond (discussed in Section 15.6), which links amino acids in a protein. 

The probable structure of one of the components of RNR and its mode of action leading to the formation of the tyrosinyl radical 122 (TyO") bound to the protein are represented on the next page (left part). The right part of the scheme concerns the hydroxylation of methane (RH = CH4). Note that the active species has the Fe =0 structure that is very similar to the one of cyctochrome P450 in the hemic series. 

In the next pages the synthesis of C-terminal lipidated peptides corresponding to Ras and Rab proteins will be described in detail. First of all, the synthesis of the required building blocks will be shown followed by different solid-phase strategies for the synthesis of a large variety of monolipidated, double lipidated, labeled, or differently functionalized peptides. 

A third class, Chlorophyta, the green seaweeds, play an important role at all Pacific coasts for regional consmnption as food and feed. Moreover, the species Chlorella and Scenedesmus have been thoroughly studied for cultivation in aquaculture as sources for fats and proteins. The economically most important organisms and their geographical distribution are listed in the table (next page). 

The Structure of DNA Elucidation of the three-dimensional structure of DNA helped researchers understand how this molecule conveys information that can be faithfully replicated from one generation to the next. Tb see the secondary structure of double-stranded DNA, go to the Protein Data Bank website (www.rcsb.org pdb). Use the PDB identifiers listed below to retrieve the data pages for the two forms of DNA... 

Finally, the goal of this first phase is to analyze and to compare the resulting proteins and peptides by alignment search tools, such as BLAST (http / blast.ncbi.nlm.nih.gov/Blast.cgi CMD=Web PAGE TYPE=BlastHome), in order to identify and characterize specific peptide fingerprints, which will be used in the monitoring approach of the next phase of the pipeline. 

Figure 3. Selection of ECP subpopulations forjprogressive iterations of the cascade procedure by silver stained SDS-PAGE. Lane 2 in each panel shows the entire ECP mixture used as the column load and lane 3 shows the column flowthrough fraction used for the next injection. Panel A demonstrates the affinity chromatography performed with day 14 antisera, Panel B with day 28 antisera and Panel C with day 42 antisera. The arrow shows ECPs depleted by the early antibodies. The progression of the immune response is clearly apparent although it is clear not all of these proteins are equally immunogenic. A 50 Kd protein has saturated its respective antibody and begun to flow through the column (Panel C, lane 4). Reproduced with permission from Ref. 24. Copyright 1989 The Humana Press Inc.

Over the next few pages you will meet the score of protein players in the game of blood clotting and learn a bit about their roles. Like members of a sports team, some of the players have strange names. Don t worry if the names or the roles of the protein quickly slip your mind—the purpose of the discussion is not for you to memorize trivia. (Besides, the names and relationships will all be shown in Figure 4-3.) Rather, my purpose is to help you get a feel for the complexity of blood clotting and to determine if it could have arisen step by step. 

A new protein, freshly made in the cell, encounters many molecular machines. Some of the machines grab hold of the protein and send it along to the location it is destined to reach. In a little while I will follow a protein along one pathway from start to finish. Protein machines all have rather exotic names, however, and it is difficult for many people to picture these things in their minds if they are not used to thinking about them. So I will first use an analogy, which will take the next several pages. 

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