Three domains of life—structure and function (Bacteria, Archaea, Eucarya)

Signal recognition particle (SRP) is an RNA and protein complex that exists in all domains of life. It consists of one protein and one noncoding RNA in some bacteria. It is more complex in eukaryotes and consists of six proteins and one noncoding RNA in mammals. In the eukaryotic cytoplasm, SRP co-translationally targets proteins to the endoplasmic reticulum and prevents misfolding and aggregation of the secretory proteins in the cytoplasm. It was demonstrated recently that SRP also possesses an earlier unknown function, the protection of mRNAs of secretory proteins from degradation. In this review, we analyze the progress in studies of SRPs from different organisms, SRP biogenesis, its structure, and function in protein targeting and mRNA protection.

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Srs2 and Pif1 as Model Systems for Understanding Sf1a and Sf1b Helicase Structure and Function

Genes ◽

10.3390/genes12091319 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1319

Author(s):

Aviv Meir ◽

Eric C. Greene

Keyword(s):

Saccharomyces Cerevisiae ◽

Nucleic Acids ◽

Model Organism ◽

Structure And Function ◽

Model Systems ◽

Genome Integrity ◽

Repair Pathway ◽

Domains Of Life ◽

Nucleoprotein Complexes ◽

And Function

Helicases are enzymes that convert the chemical energy stored in ATP into mechanical work, allowing them to move along and manipulate nucleic acids. The helicase superfamily 1 (Sf1) is one of the largest subgroups of helicases and they are required for a range of cellular activities across all domains of life. Sf1 helicases can be further subdivided into two classes called the Sf1a and Sf1b helicases, which move in opposite directions on nucleic acids. The results of this movement can range from the separation of strands within duplex nucleic acids to the physical remodeling or removal of nucleoprotein complexes. Here, we describe the characteristics of the Sf1a helicase Srs2 and the Sf1b helicase Pif1, both from the model organism Saccharomyces cerevisiae, focusing on the roles that they play in homologous recombination, a DNA repair pathway that is necessary for maintaining genome integrity.

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Social Life: Structure and Function; An Introductory General Sociology.

American Sociological Review ◽

10.2307/2086930 ◽

1950 ◽

Vol 15 (5) ◽

pp. 683

Author(s):

W. R. Goldschmidt ◽

John W. Bennett ◽

Melvin Tumin

Keyword(s):

Social Life ◽

Structure And Function ◽

And Function ◽

Life Structure

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Social Life: Structure and Function

The American Catholic Sociological Review ◽

10.2307/3706863 ◽

1949 ◽

Vol 10 (2) ◽

pp. 123

Author(s):

Sister Mary Edward ◽

John W. Bennett ◽

Melvin M. Tumin

Keyword(s):

Social Life ◽

Structure And Function ◽

And Function ◽

Life Structure

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Existence of theoretical ribosomal protein mass fingerprints in bacteria, archaea and eukaryotes

10.7287/peerj.preprints.26511v1 ◽

2018 ◽

Author(s):

Wenfa Ng

Keyword(s):

Mass Spectrometry ◽

Ribosomal Protein ◽

Molecular Mass ◽

Ribosomal Proteins ◽

General Structure ◽

Structure And Function ◽

Microbial Identification ◽

Protein Mass ◽

Domains Of Life ◽

And Function

Ribosomes are highly conserved given the importance of protein synthesis to cell survival. Although small differences in structure and functions exists in ribosomes from different species of bacteria, archaea and eukaryotes, the general structure and function remains conserved across species in the same domain of life. Thus, are ribosomal proteins that constitute ribosomes highly conserved between species in the same domain or do they possess sufficient sequence variation that help identify individual species? Having differentiated sequence would mean that ribosomal proteins from different species might account for differences in structure and function of the ribosomes in different species. Using ribosomal protein amino acid sequence information from Ribosomal Protein Gene Database for calculating molecular mass of ribosomal proteins, this study sought to determine if the molecular mass of a set of ribosomal proteins from a species could constitute a unique ribosomal protein mass fingerprint. In addition, the question of whether unique ribosomal protein mass fingerprint exists between different species in the three domains of life was also examined. Results revealed that distinct molecular mass of individual ribosomal protein could aggregate into a unique ribosomal protein mass fingerprint for individual bacterial, archaeal and eukaryotic species. Such ribosomal protein mass fingerprints could potentially find use in microbial identification through gel-free matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling of solubilized ribosomal proteins. Obtained ribosomal protein mass spectrum could be compared with those catalogued in a reference database of known microorganisms where pattern recognition algorithms could determine a match. Additionally, existence of theoretical ribosomal protein mass fingerprint across species in the three domains of life also pointed to the presence of small differences in structure and function of both the large and small ribosome subunit. Such differences could reveal possible differentiated ribosomal structure and function in different species even though the general structure and function of the ribosome is conserved across species. Collectively, distinct molecular mass of individual ribosomal proteins in species pointed to a unique ribosomal protein mass fingerprint that could find use in microbial identification through gel-free mass spectrometry analysis of solubilized ribosomal proteins. Differences in mass of ribosomal proteins across species also highlighted existence of ribosomes of differentiated structure and function between different species even though the general structure and function of the ribosome remains highly conserved.

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Existence of theoretical ribosomal protein mass fingerprints in bacteria, archaea and eukaryotes

10.7287/peerj.preprints.26511 ◽

2018 ◽

Author(s):

Wenfa Ng

Keyword(s):

Mass Spectrometry ◽

Ribosomal Protein ◽

Molecular Mass ◽

Ribosomal Proteins ◽

General Structure ◽

Structure And Function ◽

Microbial Identification ◽

Protein Mass ◽

Domains Of Life ◽

And Function

Ribosomes are highly conserved given the importance of protein synthesis to cell survival. Although small differences in structure and functions exists in ribosomes from different species of bacteria, archaea and eukaryotes, the general structure and function remains conserved across species in the same domain of life. Thus, are ribosomal proteins that constitute ribosomes highly conserved between species in the same domain or do they possess sufficient sequence variation that help identify individual species? Having differentiated sequence would mean that ribosomal proteins from different species might account for differences in structure and function of the ribosomes in different species. Using ribosomal protein amino acid sequence information from Ribosomal Protein Gene Database for calculating molecular mass of ribosomal proteins, this study sought to determine if the molecular mass of a set of ribosomal proteins from a species could constitute a unique ribosomal protein mass fingerprint. In addition, the question of whether unique ribosomal protein mass fingerprint exists between different species in the three domains of life was also examined. Results revealed that distinct molecular mass of individual ribosomal protein could aggregate into a unique ribosomal protein mass fingerprint for individual bacterial, archaeal and eukaryotic species. Such ribosomal protein mass fingerprints could potentially find use in microbial identification through gel-free matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling of solubilized ribosomal proteins. Obtained ribosomal protein mass spectrum could be compared with those catalogued in a reference database of known microorganisms where pattern recognition algorithms could determine a match. Additionally, existence of theoretical ribosomal protein mass fingerprint across species in the three domains of life also pointed to the presence of small differences in structure and function of both the large and small ribosome subunit. Such differences could reveal possible differentiated ribosomal structure and function in different species even though the general structure and function of the ribosome is conserved across species. Collectively, distinct molecular mass of individual ribosomal proteins in species pointed to a unique ribosomal protein mass fingerprint that could find use in microbial identification through gel-free mass spectrometry analysis of solubilized ribosomal proteins. Differences in mass of ribosomal proteins across species also highlighted existence of ribosomes of differentiated structure and function between different species even though the general structure and function of the ribosome remains highly conserved.

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Development of inhibitors as research tools for carbohydrate-processing enzymes

Biochemical Society Transactions ◽

10.1042/bst20120201 ◽

2012 ◽

Vol 40 (5) ◽

pp. 913-928 ◽

Cited By ~ 11

Author(s):

Tracey M. Gloster

Keyword(s):

Present Article ◽

Enzyme Inhibitors ◽

Structure And Function ◽

Glycoside Hydrolases ◽

Processing Enzymes ◽

Cellular Processes ◽

Domains Of Life ◽

And Function ◽

Complex Glycan ◽

Synthesis And Degradation

Carbohydrates, which are present in all domains of life, play important roles in a host of cellular processes. These ubiquitous biomolecules form highly diverse and often complex glycan structures without the aid of a template. The carbohydrate structures are regulated solely by the location and specificity of the enzymes responsible for their synthesis and degradation. These enzymes, glycosyltransferases and glycoside hydrolases, need to be functionally well characterized in order to investigate the structure and function of glycans. The use of enzyme inhibitors, which target a particular enzyme, can significantly aid this understanding, and may also provide insights into therapeutic applications. The present article describes some of the approaches used to design and develop enzyme inhibitors as tools for investigating carbohydrate-processing enzymes.

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Structure and function of neural networks in the retina

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100102213 ◽

1988 ◽

Vol 46 ◽

pp. 26-27

Author(s):

Peter Sterling

Keyword(s):

Ganglion Cells ◽

Three Dimensional ◽

Structure And Function ◽

Synaptic Connections ◽

Visual Axis ◽

One Dimensional ◽

Cat Retina ◽

Ultrathin Sections ◽

And Function ◽

Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

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Osseointegration interface of calcified bone and endosseous implants

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100130110 ◽

1992 ◽

Vol 50 (2) ◽

pp. 1096-1097

Author(s):

K.E. Krizan ◽

J.E. Laffoon ◽

M.J. Buckley

Keyword(s):

Structure And Function ◽

Titanium Implants ◽

En Bloc ◽

Endosseous Implants ◽

Ultrastructural Studies ◽

The Past ◽

Cacodylate Buffer ◽

One Year ◽

And Function

With increase use of tissue-integrated prostheses in recent years it is a goal to understand what is happening at the interface between haversion bone and bulk metal. This study uses electron microscopy (EM) techniques to establish parameters for osseointegration (structure and function between bone and nonload-carrying implants) in an animal model. In the past the interface has been evaluated extensively with light microscopy methods. Today researchers are using the EM for ultrastructural studies of the bone tissue and implant responses to an in vivo environment. Under general anesthesia nine adult mongrel dogs received three Brånemark (Nobelpharma) 3.75 × 7 mm titanium implants surgical placed in their left zygomatic arch. After a one year healing period the animals were injected with a routine bone marker (oxytetracycline), euthanized and perfused via aortic cannulation with 3% glutaraldehyde in 0.1M cacodylate buffer pH 7.2. Implants were retrieved en bloc, harvest radiographs made (Fig. 1), and routinely embedded in plastic. Tissue and implants were cut into 300 micron thick wafers, longitudinally to the implant with an Isomet saw and diamond wafering blade [Beuhler] until the center of the implant was reached.

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