Ribosomes, continued structure

Fig. 9-18 The tryptophan operon and its reguiation showing the situation with moderateiy iow concentrations of tryptophan. The terminator structure forms when the ribosome continues transiation past the trp codons in the ieader peptide and biocks region 2. With criti-caiiy iow concentrations of tryptophan, the ribosome staiis at trp codons, favoring formation of a stem ioop structure that permits transcription to continue.

A ribosome begins to synthesize the leader peptide, but stalls at the histidine codons because it cannot readily find histidine. Because the ribosome is covering up a different part of the mRNA, the message wiU not fold into the correct terminator structure, and RNA polymerase continues transcription through the structural genes of the operon. Translation of the message produces all the enzymes of the histidine biosynthetic pathway. 

The hierarchy of protein structure is illustrated in hgure 11.4. Here too we have a wealth of structural information. The quaternary structures for many proteins are now known and generally available in databases. As complex as these are, this is not the end of the story. We have atom-by-atom structures for entities as complex as viruses and the ribosome, an intracellular RNA-protein complex and the site of protein synthesis. Modem structural biology continues to provide detailed insights into some of the most complex constracts of nature. We are better off for having these insights. 

The nucleus is separated from the cytoplasm by the nuclear envelope, which consists of the outer and inner nuclear membranes. Each of the two nuclear membranes has two layers, and the membranes are separated from each other by the perinuclear space. The outer nuclear membrane is continuous with the rough endoplasmic reticulum and is covered with ribosomes. The inner side of the membrane is covered with a protein layer (the nuclear lamina), in which the nuclear structures are anchored. 

The known catalytic repertoire of ribozymes continues to expand. Some virusoids, small RNAs associated with plant RNA viruses, include a structure that promotes a self-cleavage reaction the hammerhead ribozyme illustrated in Figure 26-25 is in this class, catalyzing the hydrolysis of an internal phosphodiester bond. The splicing reaction that occurs in a spliceosome seems to rely on a catalytic center formed by the U2, U5, and U6 snRNAs (Fig. 26-16). And perhaps most important, an RNA component of ribosomes catalyzes the synthesis of proteins (Chapter 27). 

When tryptophan levels are high, the ribosome quickly translates sequence 1 (open reading frame encoding leader peptide) and blocks sequence 2 before sequence 3 is transcribed. Continued transcription leads to attenuation at the terminator-like attenuator structure formed by sequences 3 and 4. 

As the mRJSlA leaves the cell nucleus in which it was created and enters the cytoplasm, it binds with specialized structures called ribosomes, as shown in Figure 13.36. Ribosomes are microscopic complexes of rRNA and proteins, and they are the site where proteins are built. As the mRNA is scrolled sequentially over the ribosome, the anticodon end of a free tRNA molecule binds to an mRNA codon. In this manner, tRNA molecules and their tag-along amino acids are placed adjacent to one another along the mRNA strand. The amino acids then chemically bond with one another, forming a long polypeptide chain that breaks away from the tRNA as it forms. This process continues until a stop mRNA codon, for which there are no tRNA anticodons, is encountered. At this point, the primary structure of a new protein has been built. 

Fig. 2. Attenuation of the trp operon. (a) When tryptophan is plentiful, sequences 3 and 4 base-pair to form a 3 4 structure that stops transcription (b) when tryptophan is in short supply, the ribosome stalls at the trp codons in sequence 1, leaving sequence 2 available to interact with sequence 3. Thus a 3 4 transcription terminator structure cannot form and transcription continues.

The NE is an elaborate structure that can be divided into several distinct sub-domains the nuclear pore complexes (NPCs), the lamin polymer, and a double membrane system consisting of the outer nuclear membrane (ONM), inner nuclear membrane (INM), lumen, and pore membrane (PoM) together with their integral proteins (Figure 1 see colour insert). The ONM is not only continuous with the ER, but is also studded with ribosomes indicating that in addition to being the outermost layer of the nucleus it is also a subcompartment of the ER. How much of its complement of integral membrane proteins is unique from more distal ER... 

Liver cells comprise the cell nucleus (= karyoplasm) and the cell body (= cytoplasm). Hepatocytes and sinusoidal cells have various types of organelles in their eosinophilic cytoplasm such as endoplasmic reticulum, Golgi apparatus, lysosomes, mitochondria, peroxisomes, ribosomes, centrioles and kinetosomes. Numerous and diverse metabolic processes take place with their help. Almost all cytoplasmic structures of liver cells are continuously renewed (up to twice daily). (20, 27, 30, 33, 35, 46-48, 50, 53, 58, 59, 69, 74) (s. figs. 2.9, 2.16-2.18) (s. tab. 2.1)... 

Cytoplasm - The cytoplasm, or protoplasm, of bacterial cells is where the functions for cell growth, metabolism, and replication are carried out. It is a gellike matrix composed of water, enzymes, nutrients, wastes, and gases and contains cell structures such as ribosomes, a chromosome, and plasmids. The cell envelope encases the cytoplasm and all its components. Unlike the eukaryotic (true) cells, bacteria do not have a membrane enclosed nucleus. The chromosome, a single, continuous strand of DNA, is localized, but not contained, in a region of the cell called the nucleoid. All the other cellular components are scattered throughout the cytoplasm. 

NAtrp levels in the cell are low because tryptophan is limiting, then ribosomes pause at a pair of tryptophan codons in the RNA. This transient ribosomal pausing allows time for an alternate hairpin structure to form in the nascent RNA which disrupts the transcriptional termination signal and RNA polymerase is able to continue down the DNA template and complete transcription (Fig. 28.11). 

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