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Selenocysteine and pyrrolysine are building blocks for polypeptides

Posted by star on 2019-03-22 00:08:47
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By the mid-1980s, there was general agreement that the protein synthetic machinery uses just 20 amino acid building blocks to make proteins. Many modified amino acids were known to be present in proteins but these were formed by modifying amino acid residues after the polypeptide chain was formed. Therefore, it was a great surprise when selenocysteine (Sec) was identified as the 21st amino acid. This rare amino acid, an analog of cysteine in which the element selenium replaces sulfur, is present in a few proteins, mostly oxidoreductases, from eukaryotes, bacteria, and archaeons.
The bacterial pathway for selenocysteyl-tRNASec formation, which was elucidated largely through the efforts of August Böck and coworkers beginning in 1986. The three steps in this pathway are as follows: (1) Selenophosphate synthetase catalyzes the synthesis of selenophosphate from ATP and selenide, (2) Ser-tRNA synthetase attaches a séryl group to tRNASec, and (3) Selenocysteine synthase catalyzes a pyridoxal phosphate- dependent conversion of selenophosphate and Ser-tRNASec to selenocystcyl- tRNASec. The tRNASec species contains up to 100 nucleotides, making it the longest known tRNA. It also has other unusual features. For example, it has one more nucleotide base pair in its acceptor arm than most other tRNAs and an extended D-arm. Because of these unique features, selenocysteyl- tRNASec is not recognized by elongation factor 1A (EF1A) (see Chapter 20), and requires its own special elongation factor.
A second unusual amino acid building block, pyrrolysine, was independently discovered by Joseph A. Krzycki and coworkers and Michael K. Chan and coworkers in 2002. Although details of the pathway for pyrrolysine -tRNA formation must still be worked out preliminary data suggest that lysine is first attached to a special tRNA and then modified. Thus far, pyrrolysine has only been observed in archaeons tha......


Several research groups initiated programs to determine tRNA's tertiary structure in the late 1960s. Progress was quite slow at first because of the difficulty in obtaining crystals that were satisfactory for x-ray diffraction analysis. Finally, in 1974 two independent research groups, one led by Alexander Rich and the other by Aaron Klug, obtained crystals of yeast tRNAphe that were suitable for x-ray diffraction analysis. The crystal structure showed that the cloverleaf folds into an L-shape. The D and anticodon arms stack to form one section of the L, while the acceptor and Т?С arms ?tасk to form the other section.
The tRNA molecule's tertiary structure is stabilized by complex interactions. Helical regions in the acceptor, anticodon, D, and Т?С arms are usually stabilized by Watson-Crick base pairing as well as by non-Watson- -Crick base pairing such as the G : U pair in the tRNAphe acceptor arm. Non-helical regions of the tRNA molecule are stabilized by hydrogenbonding interactions between two or three bases that are not usually considered to be complementary to one another and by hydrogenbonding interactions that involve the 2'-hydroxyl group in ribose. 2'-Hydroxyl interactions are especially interesting because they cannot occur in DNA molecules. Different tRNAs have a similar folding pattern, ensuring that various components of the protein synthetic machinery will be able to recognize the tRNA after an amino acid has been attached to it. However, tRNAs also must have unique features that can be recognized by aminoacyl-tRNA synthetases.



New ways to detect cancer

Posted by star on 2019-03-17 19:30:35
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    Researchers in the United States have developed a new way to detect cancer cells. With a new blood test, they can determine a patient's condition by identifying the pieces of DNA characteristic of cancer cells released into the blood after they have been cleaved. The technique is sensitive and accurate enough to detect individual "outliers" in hundreds of millions of healthy blood cells.
    The mortality rate of cancer is extremely high. It is particularly important to detect the early signs of cancer. However, the high cost of money and time actually makes ordinary people feel inconvenient. A simple blood test that can pick up signs of cancer proliferation is a quick fix for many people. Scientists believe that tumors need blood to grow, and that blood may contain information left behind by cancer cells. "It's a liquid-like biopsy that avoids pain and is a better way for doctors to monitor the development of cancer cells than a conventional imaging scan," said Dr. Robert Haber, director of the cancer center at Massachusetts general hospital, who was involved in the test.

    This idea has encountered many difficulties in practical operation. It is generally believed that in both cases, the proliferation of cancer cells is at a mild stage. Therefore, the amount of DNA samples is small compared with the amount of DNA in normal blood. Therefore, it is very difficult to find the mutated DNA. In addition to DNA mutations, scientists think they can be detected through epigenetics. Scientists believe that different tissues leave different methylation modifications on DNA, and analyzing the degree of DNA methylation modification can infer the source of DNA. They tested this idea and effectively detected circulating tumor DNA by analyzing methyl......


    RNA's involvement in polypeptide synthesis, which is taken for granted today, was not firmly established until the 1950s. The earliest clues that RNA plays some role in information flow between genes and polypeptides came from the independent work of Torbjörn Caspersson and Jean Brachet in the late 1930s and early 1940s. Caspersson used cytochemical techniques to show that: (1) most of a eukaryotic cell's DNA and RNA are in its nucleus and cytoplasm, respectively; (2) cells that are actively engaged in protein synthesis have high levels of cytoplasmic RNA; and (3) cytoplasmic RNA tends to be concentrated in small spherical particles. Brachet, using cell fractionation techniques to separate nuclear and cytoplasmic fractions, also observed a correlation between active protein synthesis and high cytoplasmic RNA levels. In addition, Brachet centrifuged the cytoplasmic fraction at high speed to obtain a pellet containing the RNA-rich spherical particles that Caspersson had observed in the cell. Because these RNA-rich particles contained tightly bound proteins, they are more properly described as ribonucleoproteins. By the early 1950s, electron microscopy techniques had improved to the point where they could be used to visualize the spherical ribonucleoprotein particles, which appeared to be about 250 Å in diameter. These particles were known by a variety of different names until 1957, when Richard B. Roberts coined the now universally accepted term ribosome.
    Some eukaryotic ribosomes appear to be free in the cytoplasm, whereas others are attached to the outer surface of a continuous intracellular tubular membrane network that Keith Porter named the endoplasmic reticulum. Regions of the ER that are studded with ribosomes appear rough or grainy in electron micrographs and are therefore known as the rough endoplasmic; reticulum (RER). Regions that lack ribosomes have a smooth appearance and are therefore called the sm......

Chloroplast DNA is also transcribed to form mRNA, rRNA, and tRNA

Posted by star on 2019-03-13 19:20:26
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In green plants, RNA synthesis takes place is a second organelle, the chloroplast, which is the site of all photosynthetic reactions. Each chloroplast has an outer membrane that separates the chloroplast from the cytoplasm and an inner membrane that surrounds a compartment called the stroma. Chloroplast DNA and the chloroplast protein synthetic machinery are present in the stroma.

The stroma also contains flat membranous sacs called thylakoids, which appear to be surrounded by a single continuous membrane that is the site of light-dependent photosynthetic reactions. The Chloroplast is believed to have originated as a cyanobacterial cell that somehow entered a eukaryotic cell. Because the cyanobacterial chromosome codes for more than 3000 different polypeptides and chloroplast DNA codes for only about 75 polypeptides, most protein coding genes were either transferred to nuclear chromosomes or lost during evolution. This transfer or loss probably took place very early in plant evolution because chloroplasts of evolutionarily distant green plants have similar gene content and organization. All chloroplasts arise from pre-existing chloroplasts.

Chloroplast DNA is a circular double-stranded negative supercoil that is about 120 to 180 kbp long. A typical chloroplast many contain as few as ten or as many as a few hundred DNA copies that are organized into nucleoids associated with the inner chloroplast membrane. In addition to their protein coding genes, Chloroplast DNA from higher plants also contain four rRNA genes and 30 tRNA genes. No RNA is imported into chloroplast. Chloroplast genes of higher green plants often contain a single groupⅠor groupⅡintron.

Chloroplast DNA codes for an RNA polymerase that resembles the bacterial core RNA polymerase (α2ββ’)and contains homologous subunits to α, β, and β’. The plastid encoded RNA polymerase(PEP)requires the assistance of a transcription factor that resemb......

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