Protein in eukaryotes

Glomset, J. A., Gelb, M. H., and Farnswordi, C. C., 1990. Prenyl proteins in eukaryotic cells A new type of membrane anchor. Trends in Biochemical Sciences 15 139—142. 

Figure 3.7 The three systems involved in the generation of Fe-S proteins in eukaryotes. (From Lill et al., 2006. Copyright 2006, with permission from Elsevier.)...

Similar sequences that bind repressor proteins in eukaryotes are called silencers. There are fewer examples of these sequences known, and the mechanisms through which they act are not clear. 

Although free amino acids and those in proteins in eukaryotes are entirely of the L-form (except glycine, which is not optically active), D-amino acids do occur in nature, for example in bacterial cell walls (D-alanine and D-glutamate). Consequently, they enter the body from bacteria in food and from the digestion of bacteria in the... 

Actin, the most abundant protein in eukaryotic cells, is the protein component of the microfilaments (actin filaments). Actin occurs in two forms—a monomolecular form (C actin, globular actin) and a polymer (F actin, filamentous actin). G actin is an asymmetrical molecule with a mass of 42 kDa, consisting of two domains. As the ionic strength increases, G actin aggregates reversibly to form F actin, a helical homopolymer. G actin carries a firmly bound ATP molecule that is slowly hydrolyzed in F actin to form ADR Actin therefore also has enzyme properties (ATPase activity). 

Results of cell biological, biochemical, and immunological research of the past decades have revealed that glycosylation is a very common posttranslational modification of proteins in eukaryotic cells [1]. The carbohydrate portions of glycoproteins obviously play important roles in the organized distribution of these macromolecules within the cells and... 

The E. coli single-strand binding protein, another helix-destabilizing protein that is usually called simply SSB, is a tetramer of 18.5-kDa subunits.265,3,2,313 It is essential to DNA replication. About 35 nucleotides may bind to each tetramer.314 The situation is not as clear in eukaryotes where DNA is largely coiled around histones in the nucleosomes. Several singlestrand binding proteins have been identified,315 but the need for SSB proteins in eukaryotic nuclear replication is uncertain.316 A human mitochondrial SSB resembles that of E. coli.317... 

As any elementary textbook on molecular biology will relate, the sequences of proteins are stored in DNA in the form of a triplet code. Each amino acid is encoded by one or more triplet combinations of the four bases A, T, G, and C. For example, tryptophan is coded by the sequence TGG. The sequence of triplets is converted into a protein by a process in which DNA is first transcribed into mRNA. This message is then translated into protein on the ribosomes in conjunction with tRNA and the aminoacyl-tRNA synthetases. In prokaryotes, there is a one-to-one relationship between the sequence of triplets in the DNA. and the sequence of amino acids in the protein. In eukaryotes, the DNA often contains stretches of intervening sequences or introns which are excised from the mRNA after transcription (Chapter 1). 

Many of the chaperones double as heat shock-proteins (Hsp). When a cell is put under stress that can cause proteins to denature, such as too high a temperature, it produces heat-shock proteins. Their names are abbreviated to Hsp plus their subunit molecular mass in kDa. Hsp70, for example, is a ubiquitous heat-shock protein in eukaryotes. It is known in E. coli as DnaK for historical reasons because it was first discovered from a supposed role in DNA replication. Hsp70 is also important in protein trafficking and the conveying of proteins across membranes, because the denatured state is important in these processes. In protein biosynthesis, the unfolded state of the nascent polypeptide chain is passed on to DnaK, which maintains it in an extended form. The chain, under the influence of ATP and co-chaperones such as DnaJ and GrpE, is handed over to GroEL. 

The control and expression of protein in eukaryotic cells is more complex than in bacteria. Research into this field is ongoing and, as such, is beyond the scope of this text. Many systems of control are known in bacteria and can be used to illustrate the type of control mechanisms and the importance of the environmental control of protein synthesis. The first and best documented example is that of the lactose (lac) operon is Escherichia coli. 

The tertiary structure of DNA is complex. DNA does not normally exist as a straight linear polymer, but as a supercoiled structure. Supercoiiing is associated with special proteins in eukaryotic organisms. Prokaryotic organisms have one continuous molecule white eukaryotes have many (e.g. humans have 46). Viruses also contain nucleic acids and their genetic material can be either DNA or RNA. 

In the previous chapter we discussed DNA-binding proteins that regulate transcription in prokaryotes. The principles that govern recognition between proteins in eukaryotes show some similarities and some differences. In both cases specific recognition is dominated by interactions that take place in the major groove of the DNA. The specific interactions usually involve H bond formation... 

In cells, DNA is always associated with proteins, in eukaryotic cells with the nucleoproteins. This packaging will further reduce the mobility of DNA segments that may carry a free radical, and their recombination with concomitant cross-linking is further slowed down. This will allow chemical repair processes such as H-donation by GSH to take place (Sect. 12.12). 

Aconitase is the trivial name for citrate dehydratase cw-aconitate hydratase (EC 4.2.1.3). It catalyzes the reversible isomerization reaction of citrate into isocitrate via the intermediate cA-aconitate (Figure 2). It is a water-soluble, monomeric protein. In eukaryotic cells aconitase is located in the mitochondrial matrix. In prokaryotes the enzyme occurs in the cytoplasma. The pig heart enzyme consists of 754 amino-acid residues, providing a molecular mass of 83 kDa [27], Aconitase from other sources has similar size. The porcine protein is synthesized with a mitochondrial targeting sequence. The mature, functional protein can be (over)expressed in Escherichia coli [28],... 

Davidson, J. N., and Peterson, M. L. (1997). Origin of genes encoding multi-enzymatic proteins in eukaryotes. Trends Genet., 13, 281-285. 

Protein phosphorylation dephosphorylation regulates the activity of enzymic and nonenzymic proteins in eukaryotic cells. Ten per cent or more of all proteins in a cell are modified in that way. The phosphates are transferred from ATP and esterified with hydroxyl groups of serine, threonine, or tyrosine residues. They are removed and transferred to water by phosphatases. There are at least about 2000 kinases and about 1000 phosphatases to carry out these reactions (Fig. 7.1). ... 

La Roche, J., Geider, R. J., Graziano, L. M., Murray, H., Lewis, K. (1993). Induction of specific proteins in eukaryotic algae grown imder iron-, phosphorus-, or nitrogen-deficient conditions. J. Phycol 29, 767-777. 

Steroid hormones can increase and decrease the level and/or activity of a large number of proteins in eukaryotes. Steroid hormones were first discovered in humans, where they play essential roles in development, differentiation, homeostasis, and endocrine therapies. However, current interest in steroid hormones is increasing because they constitute excellent model systems for examining the control of gene expression. Many human pathologies result from the inappropriate expression of protein(s). Thus, to treat disease states, it is critical to understand the normal processes governing how, when, and how much of the information encoded in the DNA of cells is transcribed to mRNAs and eventually into proteins, which perform most of the functions of cells. Steroid hormones provide excellent model systems with which to address these clinically relevant questions. 

Myosins, kinesins, and dyneins move by cycling between states with different affinities for the long, polymeric macromolecules that serve as their tracks. For myosin, the molecular track is a polymeric form of actin, a 42-kd protein that is one of the most abundant proteins in eukaryotic cells, typically accounting for as much as 10% of the total protein. Actin polymers are continually being assembled and disassembled in cells in a highly dynamic manner, accompanied by the hydrolysis of ATP. On the microscopic scale, actin filaments participate in the dynamic reshaping of the cytoskeleton and the cell itself and in other motility mechanisms that do not include myosin. In muscle, myosin and actin together are the key components responsible for muscle contraction. 

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