Eukaryotic systems, protein structure-function

Chapters 27. 28, and 29 cover DNA replication, recombination, and repair RNA synthesis and splicing and protein synthesis. Evolutionary connections between prokaryotic systems and eukaryotic systems reveal how the basic biochemical processes have been adapted to function in more-complex biological systems. The recently elucidated structure of the ribosome gives students a glimpse into a possible early RNA world, in which nucleic acids, rather than proteins, played almost all the major roles in catalyzing important pathways. 

A biological membranes system is typically formed by the combination of lipids and proteins. In eukaryotic cells, the plasma membrane, also referred to as the cell membrane, is a protective barrier which regulates what enters and leaves the cell. The endomembrane system is composed of different kinds of membranes which divide the cell into structural and functional compartments within a eukaryotic cell, such as the endoplasmic reticulum, Golgi apparatus, mitochondria, endosome and lysosome. Covalent modification of proteins with lipid anchors (protein lipidation) facilitates association of the lipidated proteins with particular membranes in eukaryotic cells. Protein lipidation is one of the most important protein post-translational modifications (PTMs). Studying lipidated protein function in vitro or in vivo is of vital importance in biological research. 

Initiation factors, IF catalytic proteins required for the initiation of RNA synthesis (see Ribonucleic acids) and of Protein synthesis (see). Three structurally and functionally characterized IF of E. coU are IF 1 (M, 9,000), IF 2 (M, 97,000) and IF 3 (M, 22,000 They appear to be loosely associated with the ribosomes, but can be dissociated from them with 0.5 M NH4CI or KCl, or isolated from the cytoplasm after homogenization. Some eukaryotic systems possess more than 10 IF (elF, e for eukaryotic), none of which can functionally substitute for the bacterial IF. There is thus strict class specificity in the initiation of protein synthesis. 

During the last ten years, it has become apparent that calcium-dependent papain-like peptidases called calpains (EC 3.4.22.17) represent an important intracellular nonlysosomal enzyme system [35][36], These enzymes show limited proteolytic activity at neutral pH and are present in virtually every eukaryotic cell type. They have been found to function in specific proteolytic events that alter intracellular metabolism and structure, rather than in general turnover of intracellular proteins. Calpains are composed of two nonidentical subunits, each of which contains functional calcium-binding sites. Two types of calpains, i.e., /i-calpain and m-calpain (formerly calpain I and calpain II, respectively), have been identified that differ in their Ca2+ requirement for activation. The activity of calpains is regulated by intracellular Ca2+ levels. At elevated cytoplasmic calcium concentrations, the precursor procal-pain associates with the inner surface of the cell membrane. This interaction seems to trigger autoproteolysis of procalpain, and active calpain is released into the cytoplasm [37]. 

E2 are structurally and functionally diverse. Early biochemical work by using reticulocyte system revealed five distinct proteins with properties of E2. With the advent of genome sequencing, this observation has been corroborated. Even simple eukaryotes like yeast Saccharomyces cerevisiae) have 13 genes potentially encoding E2s. The number of E2s in mammals is estimated to be in the range of 25-30. 

Ribosomal proteins Ribosomal proteins are present in considerably greater numbers in eukaryotic ribosomes than in prokaryotic ribosomes. These proteins play a number of roles in the structure and function of the ribosome and its interactions with other components of the translation system. 

Microtubules in the long axons of nerve cells function as "rails" for the "fast transport" of proteins and other materials from the cell body down the axons. In fact, microtubules appear to be present throughout the cytoplasm of virtually all eukaryotic cells (Fig. 7-32) and also in spirochetes.311 Motion in microtubular systems depends upon motor proteins such as kinesin, which moves bound materials toward what is known as the "negative" end of the microtubule,312 dyneins which move toward the positive end.310 These motor proteins are driven by the Gibbs energy of hydrolysis of ATP or GTP and in this respect, as well as in some structural details (Chapter 19), resemble the muscle protein myosin. Dynein is present in the arms of the microtubules of cilia (Fig. 1-8) whose motion results from the sliding of the microtubules driven by the action of this protein (Chapter 19). 

The engineering of eukaryotic genes in eukaryotic organisms (yeast) is still in its infancy and its application is not as well developed as that of the bacterial systems. This is due to the increased complexity encountered in the structure and function of eukaryotic chromosomes. However, many advances have been made in the development of this system, particularly for the production of materials that require post-translational modification of the protein, and where other additional materials must be added before a fully functional molecule is produced (e.g. glycoproteins). 

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