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  1. Marina Berzins McCoy
  2. Wicked Obsession
  3. Depths of Depravation
  4. Climate Change and the Emergent National Security Landscape
  5. Structural Biochemistry/Volume 2

The cell nucleus is an important organelle because it is where genes and their controlling factors are formed. In order to do so, it needs the helps of the stored components:. The nucleolus, or plural nucleoli, is normally a circular structure composed of proteins and nucleic acids.

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Nucleoli are not typical organelles for the reason that they have no lipid membrane , making it with of the few non-membrane bound organelles in the cell. The nucleolus is located within the nucleus of eukaryote cells and is in charge of producing ribosomal RNA and the arrangement of ribosomes. The structure of the nucleoli can be seen using electron microscopy and fluorescent protein tagging can be used to view the dynamics of the nucleoli. The nucleolus is the nuclear subdomain that assembles ribosomal subunits in eukaryotic cells.

The nucleolar organiser regions of chromosomes, which contain the genes for pre-ribosomal ribonucleic acid rRNA , serve as the foundation for nucleolar structure. The nucleolus disassembles at the beginning of mitosis, its components disperse in various parts of the cell and reassembly occurs during telophase and early G1 phase. Ribosome assembly begins with transcription of pre-rRNA. During transcription ribosomal and nonribosomal proteins attach to the RNA.

Subsequently, there is modification and cleavage of pre-rRNA and incorporation of more ribosomal proteins and 5S rRNA into maturing pre-ribosomal complexes.

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The nucleolus also contains proteins and RNAs that are not related to ribosome assembly and a number of new functions for the nucleolus have been identified. These include assembly of signal recognition particles, sensing cellular stress and transport of human immunodeficiency virus 1 HIV-1 messenger RNA.

In eukaryotes, ribosomes can commonly be found in the cytosol of a cell, the endoplasmic reticulum or mRNA , as well as the matrix of the mitochondria. Proteins synthesized in each of these locations serve a different role in the cell. In prokaryotes ribosomes can be found in the cytosol as well.

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This protein-synthesizing organelle is the only organelle found in both prokaryotes and eukaryotes, asserting that the ribosome was a trait that evolved early on, most likely present in the common ancestor of eukaryotes and prokaryotes. Ribosomes are not membrane bound.

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Ribosomes are also play a key role in the catalysis of two important and crucial biological processes. They are responsible for peptidyl transfer, in which they form peptide bonds during protein synthesis as well as peptidyl hydrolysis; in this process, the ribosome releases the completely formed protein from the peptidyl transfer RNA after completion of translation.

Translation is the process of converting mRNA from transcription to functional proteins; The three steps involved are initiation, elongation, and termination. Proteins are translated one amino acid three base pairs at a time. During this process, tRNA assists the ribosome by bringing the complementary bases to the ribosome as translation proceeds.

Because ribosome synthesis is a major metabolic activity that involves hundreds of individual reactions in eukaryotes, errors will occur eventually during these processes. To deal with the error in ribosome synthesis if it occurs, eukaryotes will degrade the erroreous ribosomes. In addition, not only the erroneous ribosomes will be degraded but also the excess ribosomes. Recent researches show that eukaryote cells enhanced many strategies to recognize specific dysfunctional or functionally deficit ribosomes for degradation [1].

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Along with having more complicated assembly regulations than bacterial ribosomes, eukaryotic ribosomes are triggered differently then bacterial ribosomes in translation initiation. Eukaryotic ribosomes use a scanning mechanism and require at least nine initiation factors. In the bacterium E. Ribosomes usually comprise 2 protein subunits and some component of rRNA. The protein componenet of the ribosomes is first synthesized in the cytosol much like any other protein.

The newly synthesized protein subunits are then transported from the nucleus into the nucleolus, the center of ribosomal RNA transcription. Cells that have a high rate of protein synthesis have many ribosomes. In the past, scientists studied ribosome to get a better understanding about its components, which is consists of 30S, 50S, 70S, and S. All are made of by the same particles but different concentration of Mg ions.

Ribosomal structure varies between eukaryotes and prokaryotes. Eukaryotes have 40S small and 60S large subunits, together the subunits form the 80S ribosome. These subunits work together during translation to synthesize proteins. In prokaryotes, the small subunit 30S and the large subunit 50S together make the 70S ribosome. Its function is to decode and decipher mRNA to determine the corresponding amino acid to the three bases in codons.

Each component can be formed separately of each other. The structural components of the small subunit have been shown to be structurally independent from each other suggesting that during protein synthesis they move and conform relative to one another. The long 44 helix stretches across the small subunit from the body to the head functioning as a potential relay for information across the entire subunit. Unlike the small subunit, the large subunit is mostly rigid with mobility restricted its peripheral regions. The mRNA binding site is located along the neck of the small subunit while the large subunit contains the peptidyl transferase center PTC where aminoacyl and peptidyl-tRNA attach.

The three binding sites are A, P, and E. Ribosome assembly consists of transcription, translation, the folding of rRNA and ribosomal proteins, the binding of ribosomal proteins, and the binding and release of the assembly components to make the ribosome. There are two intermediates in ribosome assembly, in vitro and in vivo. One method of in vitro assembly of the 30S is to only use free rRNA and ribosomal proteins. With the different ways to assemble proteins, the assembly of ribosomes also varies with different temperatures.

After completing these two processes, the RI particle together with the remaining proteins can form the 30S subunit. In contrast, the in vitro assembly of the 50S subunit requires more steps and harsher conditions compared to the assembly mechanism of the 30S. There are three reconstitution intermediates each dependent on different temperatures and ionic conditions.

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RI50 1 , the first intermediate, yields the 33S particle. The remaining proteins form the RI50 3 which create the inactive 48S particle. In order for the 48S particle to become the active 50S subunit, the temperature and concentration of magnesium needs to be increased along with the involvement of the 5S rRNA.

Like the in vitro assembly mechanism, the in vivo assembly of the 30S subunit has two intermediates pS and pS and the 50S subunit has three intermediates pS, pS, and pS. However, the reconstitution intermediates are not the same as in vitro. The intermediates of the 30S subunit yield 21S and 30S particles while the intermediates of the 50S subunit yield 32S, 43S, and 50S particles.

The intermediates in the in vivo assembly are precursor rRNA which is different from in vitro which uses matured rRNA. To complete the mechanism of ribosome assembly, these precursor rRNA gets transformed in the polysomes. A eukaryotic ribosome is composed of a 40S and 60S subunits, they both have a solvent exposed side and a subunit interface.

The solvent exposed side contains a higher concentration of protein and RNA elements that are only in eukaryotes compared to the subunit interface.

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The eukaryotic specific proteins are responsible for 40S structure being stabilized by tertiary contacts. The majority of the eukaryotic specific proteins and extensions are to interconnect other proteins in the 40S and 60S subunit. The 40S subunit has 14 of these interconnected proteins located in the head. The 60S specific extensions consist of beta sheets and long alpha helices which are crucial in long distance tertierary interaction, meaning they have the ability to interact across the subunit. This trait is unique for eukaryotes because protein-protein contact is very rare in the prokaryote ribosome.

The 40S and 60S subunits are joined by eukaryote specific inter-subunit bridges that connects them thus forming 80s. Ribosomal cofactors help facilitate with improper folding during in vitro.

Structural Biochemistry/Volume 2

The improper folding during in vitro is a cause which results in vitro being much slower than in vivo. An over expression of DEAD-box proteins can suppress the deletion of another strain.

DEAD-box proteins DBPs are characterized by a core of approximately amino acids, each containing at least 9 conserved amino acid motifs. Studies have shown that these proteins use the energy from ATP hydrolysis to rearrange inter- or intra-molecular RNA structures or dissociate RNA-proteins interactions.