Ribosome shape

Transfer RNA (tRNA) Transfer RNAs are relatively small nucleic acids containing only about 70 nucleotides They get their name because they transfer ammo acids to the ribosome for incorporation into a polypeptide Although 20 ammo acids need to be transferred there are 50-60 tRNAs some of which transfer the same ammo acids Figure 28 11 shows the structure of phenylalanine tRNA (tRNA ) Like all tRNAs it IS composed of a single strand with a characteristic shape that results from the presence of paired bases m some regions and their absence m others... 

Chloroplasts (29-36) are the sites of photosynthesis and their ribosomes can carry out protein synthesis. Chloroplasts that contain chlorophylls and carotenoids, are disc shaped and 4-6 pm in diameter. These plastids are comprised of a ground substance (stroma) and are traversed by thylakoids (flattened membranous sacs). The thylakoids are stacked as grana. In addition, the chloroplasts of green algae and plants contain starch grains, small lipid oil droplets, and DNA. 

Mitochondria (45-56) are organelles possessing a double membrane, the inner of which is invaginated as cristae. An intermembrane space exists between the inner and outer membranes. The inner membrane consists of an unusually high amount of protein and possesses spherically shaped particles approx 9 nm in diameter. These particles appear to be equivalent to F0, Fb and adenosine triphosphatase. In contrast to the inner membrane, the outer membrane is smooth and appears to be connected to the smooth er. This membrane is permeable to all molecules of 10,000 Dalton or less. A mitochondrial matrix is enclosed by the inner membrane and consists of a ground substance of particles, nucleoids, ribosomes, and electron-transparent regions containing DNA. 

Since the X-ray structural analysis of crystallized proteins yields the most direct information on the tertiary structure, many attempts have been made in the last decade to crystallize individual ribosomal proteins. However, it was many years before any progress in this field was made. The N- and C-terminal fragments of the . coU protein L7/L12 have been crystallized, and the crystals diffract to 4 and 2.6 A, respectively (Liljas et ai, 1978). According to the X-ray analysis, the C-terminal fragment (positions 53-120) has a compact, plum-shaped tertiary structure with three a helices and three p sheets (Leijonmarck et ai, 1980). 

To determine the shape of ribosomal proteins in solution, ultracentrifugation, digital densimetry, viscosity, gel filtration, quasi-elastic light scattering, and small-angle X-ray or neutron scattering have all been used. With each technique it is possible to obtain a physical characteristic of the protein. Combining these techniques should allow the size and shape of the protein to be characterized quite well. However, the values determined in various laboratories for the same ribosomal proteins differ considerably. To help understand some of the reasons we will initially discuss each method briefly as it relates to proteins and then review the size and shape of the ribosomal proteins that have been so characterized. 

In order to place the ribosomal components in the appropriate topography, the size and shape of the ribosomal subunits must be defined. 

Though solution scattering and electron microscopy can provide information on the shape and size of the ribosome and its subunits, diffraction techniques, such as X-ray analysis, are expected to yield an insight into the ribosomal structure at a much higher resolution. 

An IgG-antibody against an individual ribosomal protein binds specifically only to this protein in a ribosomal subunit. Since the antibody is divalent it can form a bridge between the identical proteins in two subunits, leading to a dimer that can be examined under Ae electron microscope. The location of the bound antibody on the subunit surface can be determined, defining the position of the antigenic determinant of a particular protein. The method relies on the fact that IgG-antibodies are able to react with specific proteins within the intact ribosomal subunits and that both subunits have discernible shapes with recognizable morphological landmarks. 

The large and small prokaryotic ribosomal subunits are SOS and 30S, respectively. The complete prokaryotic ribosome is a 70S particle. (Note The S values are determined by behavior of the particles in an ultracentrifuge. They are a function of both size and shape, and therefore the numbers are not additive.)... 

As proteins emerge from ribosomes, they fold into three-dimensional conformations that are essential for their subsequent biologic activity. Generally, four levels of protein shape are distinguished ... 

The cytosol is the fluid compartment of the cell and contains the enzymes responsible for cellular metabolism together with free ribosomes concerned with local protein synthesis. In addition to these structures which are common to all cell types, the neuron also contains specific organelles which are unique to the nervous system. For example, the neuronal skeleton is responsible for monitoring the shape of the neuron. This is composed of several fibrous proteins that strengthen the axonal process and provide a structure for the location of specific membrane proteins. The axonal cytoskeleton has been divided into the internal cytoskeleton, which consists of microtubules linked to filaments along the length of the axon, which provides a track for the movement of vesicular material by fast axonal transport, and the cortical cytoskeleton. 

In contrast to DNA, RNAs do not form extended double helices. In RNAs, the base pairs (see p.84) usually only extend over a few residues. For this reason, substructures often arise that have a finger shape or clover-leaf shape in two-dimensional representations. In these, the paired stem regions are linked by loops. Large RNAs such as ribosomal 16S-rRNA (center) contain numerous stem and loop regions of this type. These sections are again folded three-dimensionally—i.e., like proteins, RNAs have a tertiary structure (see p.86). However, tertiary structures are only known of small RNAs, mainly tRNAs. The diagrams in Fig. B and on p.86 show that the clover-leaf structure is not recognizable in a three-dimensional representation. 

The PDH complex of the bacterium Escherichia coli has been particularly well studied. It has a molecular mass of 5.3 10 , and with a diameter of more than 30 nm it is larger than a ribosome. The complex consists of a total of 60 polypeptides (1, 2) 24 molecules of E2 (eight trimers) form the almost cube-shaped core of the complex. Each of the six surfaces of the cube is occupied by a dimer of E3 components, while each of the twelve edges of the cube is occupied by dimers of El molecules. Animal oxoacid dehydrogenases have similar structures, but differ in the numbers of subunits and their molecular masses. 

The two irregularly shaped ribosomal subunits fit together to form a cleft through which the mRNA passes as the ribosome moves along it during translation (Fig. 27-9b). The 55 proteins in bacterial ribosomes vary enormously in size and structure. Molecular weights range from about 6,000 to 75,000. Most of the proteins... 

Ribosomal RNAs (rRNAs) are found in association with several proteins as components of the ribosomes—the complex structures that serve as the sites for protein synthesis (see p. 433). There are three distinct size species of rRNA (23S, 16S, and 5S) in prokaryotic cells (Figure 30.2). In the eukaryotic cytosol, there are four rRNA size species (28S, 18S, 5.8S, and 5S). [Note "S" is the Svedberg unit, which is related to the jnolecular weight and shape of the compound.] Together, rRNAs make up eighty percent of the total RNA in the cell. 

Ribosomes are large complexes of protein and rRNA (Figure 31.8). They consist of two subunits—one large and one small—whose relative sizes are generally given in terms of their sedimentation coefficients, or S (Svedberg) values. [Note Because the S values are determined both by shape as well as molecular mass, their numeric values are not strictly additive. For example, the prokaryotic 50S and 30S ribosomal subunits together form a ribosome with an S value of 70. The eukaryotic 60S and 40S subunits form an 80S ribosome.] Prokaryotic and eukaryotic ribosomes are similar in structure, and serve the same function, namely, as the "factories" in which the synthesis of proteins occurs. 

Most ribosomal proteins are rich in lysine and arginine and, therefore, carry a substantial net positive charge. Proteins S20, L7/12, and L10 have over 20% alanine, while L29 is almost as rich in leucine. Proteins S10, S13, L7/L12, L27, L29, and L30 are surprisingly low (<2 mol %) in aromatic amino acids. Proteins S5, S18, and L7 have acetylated N termini while Lll, L3, L7/12, Lll, L16, and L33 contain methylated amino acids. Lll contains nine methyl groups.22 Protein S6 is the major phosphoprotein of eukaryotic ribosomes.103104 Most ribosomal proteins have no known enzymatic activity. Although often difficult to crystallize, high-resolution three-dimensional structures are known for many free ribosomal proteins.24 Most of them have shapes resembling those previously found... 

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