Thomas S. Bianchi and Elizabeth A. Canuel
- Published in print:
- 2011
- Published Online:
- October 2017
- ISBN:
- 9780691134147
- eISBN:
- 9781400839100
- Item type:
- chapter
- Publisher:
- Princeton University Press
- DOI:
- 10.23943/princeton/9780691134147.003.0006
- Subject:
- Biology, Ecology
This chapter discusses proteins, which make up approximately 50% of organic matter and contain about 85% of the organic nitrogen in marine organisms. Peptides and proteins comprise an important ...
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This chapter discusses proteins, which make up approximately 50% of organic matter and contain about 85% of the organic nitrogen in marine organisms. Peptides and proteins comprise an important fraction of the particulate organic carbon (13–37%) and particulate organic nitrogen (30–81%), as well as dissolved organic nitrogen (5–20%) and dissolved organic carbon (3–4%) in oceanic and coastal waters. In sediments, proteins account for approximately 7 to 25% of organic carbon and an estimated 30 to 90% of total nitrogen. Amino acids are the basic building blocks of proteins. This class of compounds is essential to all organisms and represents one of the most important components in the organic nitrogen cycle. Amino acids represent one of the most labile pools of organic carbon and nitrogen.Less
This chapter discusses proteins, which make up approximately 50% of organic matter and contain about 85% of the organic nitrogen in marine organisms. Peptides and proteins comprise an important fraction of the particulate organic carbon (13–37%) and particulate organic nitrogen (30–81%), as well as dissolved organic nitrogen (5–20%) and dissolved organic carbon (3–4%) in oceanic and coastal waters. In sediments, proteins account for approximately 7 to 25% of organic carbon and an estimated 30 to 90% of total nitrogen. Amino acids are the basic building blocks of proteins. This class of compounds is essential to all organisms and represents one of the most important components in the organic nitrogen cycle. Amino acids represent one of the most labile pools of organic carbon and nitrogen.
Richard P. Evershed
- Published in print:
- 2007
- Published Online:
- January 2012
- ISBN:
- 9780197264140
- eISBN:
- 9780191734489
- Item type:
- chapter
- Publisher:
- British Academy
- DOI:
- 10.5871/bacad/9780197264140.003.0008
- Subject:
- Archaeology, Prehistoric Archaeology
The paucity of cultural finds at this key stage in human prehistory increases the need to fully and effectively exploit all the sources of evidence that exist. Organic residues, preserved in ...
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The paucity of cultural finds at this key stage in human prehistory increases the need to fully and effectively exploit all the sources of evidence that exist. Organic residues, preserved in association with skeletal remains and pottery, have the potential to provide various levels of information relating to diet and subsistence, and thus the wider interactions of ancient humans with their environment. This chapter explores the potential to enhance the rigour and level of information retrievable from the biochemical constituents of skeletal remains and pottery by exploiting new sources of molecular and isotopic information. It addresses the following possibilities: (i) deriving palaeodietary information from human remains via the complementary use of amino acid and lipid components; and (ii) assessing terrestrial and marine contributions to organic residues preserved in skeletal remains and pottery.Less
The paucity of cultural finds at this key stage in human prehistory increases the need to fully and effectively exploit all the sources of evidence that exist. Organic residues, preserved in association with skeletal remains and pottery, have the potential to provide various levels of information relating to diet and subsistence, and thus the wider interactions of ancient humans with their environment. This chapter explores the potential to enhance the rigour and level of information retrievable from the biochemical constituents of skeletal remains and pottery by exploiting new sources of molecular and isotopic information. It addresses the following possibilities: (i) deriving palaeodietary information from human remains via the complementary use of amino acid and lipid components; and (ii) assessing terrestrial and marine contributions to organic residues preserved in skeletal remains and pottery.
Dawn J. Brooks and Eric A. Gaucher
- Published in print:
- 2007
- Published Online:
- September 2008
- ISBN:
- 9780199299188
- eISBN:
- 9780191714979
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199299188.003.0017
- Subject:
- Biology, Evolutionary Biology / Genetics
The last universal ancestor (LUA) represents a relatively accessible theoretical intermediary between extant cellular organisms and early, precellular ‘life’. In a previous study, the ...
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The last universal ancestor (LUA) represents a relatively accessible theoretical intermediary between extant cellular organisms and early, precellular ‘life’. In a previous study, the expectation-maximization (EM) approach was used to infer ancestral amino acid frequencies, where in each iteration expected counts were derived from posterior distributions at each site. Applying this approach to estimate the amino acid composition of 65 proteins in the LUA showed that composition was more similar to that of extant thermophiles than mesophiles. This chapter examines whether the previous result is robust with respect to the OGT of the taxa used to infer the amino acid composition of proteins in the LUA. It is shown that even if only mesophilic species are used to derive the estimated ancestral amino acid composition, that composition is most similar to that of thermophiles, as measured by Euclidean distance. The relative mean Euclidean distance between the amino acid composition in any one species and that of a set of mesophiles or thermophiles can be used unequivocally to classify it. Thus, the inferred amino acid composition in the LUA allows its classification as a thermophile.Less
The last universal ancestor (LUA) represents a relatively accessible theoretical intermediary between extant cellular organisms and early, precellular ‘life’. In a previous study, the expectation-maximization (EM) approach was used to infer ancestral amino acid frequencies, where in each iteration expected counts were derived from posterior distributions at each site. Applying this approach to estimate the amino acid composition of 65 proteins in the LUA showed that composition was more similar to that of extant thermophiles than mesophiles. This chapter examines whether the previous result is robust with respect to the OGT of the taxa used to infer the amino acid composition of proteins in the LUA. It is shown that even if only mesophilic species are used to derive the estimated ancestral amino acid composition, that composition is most similar to that of thermophiles, as measured by Euclidean distance. The relative mean Euclidean distance between the amino acid composition in any one species and that of a set of mesophiles or thermophiles can be used unequivocally to classify it. Thus, the inferred amino acid composition in the LUA allows its classification as a thermophile.
Xun Gu, Ying Zheng, Yong Huang, and Dongping Xu
- Published in print:
- 2007
- Published Online:
- September 2008
- ISBN:
- 9780199299188
- eISBN:
- 9780191714979
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199299188.003.0011
- Subject:
- Biology, Evolutionary Biology / Genetics
This chapter presents a new approach to functional divergence analysis with the combination of ancestral sequence inference, using the family of animal G-protein subunits as an example. Using the ...
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This chapter presents a new approach to functional divergence analysis with the combination of ancestral sequence inference, using the family of animal G-protein subunits as an example. Using the method, the evolutionary trends of two types of functional divergence of amino acid residues after gene duplication are traced. These pieces of evolutionary information are useful for making testable hypotheses about functional divergence between protein subfamilies, such as subtypes of G-protein subunits, which can be verified by further experimentation.Less
This chapter presents a new approach to functional divergence analysis with the combination of ancestral sequence inference, using the family of animal G-protein subunits as an example. Using the method, the evolutionary trends of two types of functional divergence of amino acid residues after gene duplication are traced. These pieces of evolutionary information are useful for making testable hypotheses about functional divergence between protein subfamilies, such as subtypes of G-protein subunits, which can be verified by further experimentation.
ZIHENG YANG
- Published in print:
- 2006
- Published Online:
- April 2010
- ISBN:
- 9780198567028
- eISBN:
- 9780191728280
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780198567028.003.0002
- Subject:
- Biology, Evolutionary Biology / Genetics
Chapter 1 discussed continuous-time Markov chain models of nucleotide substitution and their application to estimate the distance between two nucleotide sequences. This chapter discusses similar ...
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Chapter 1 discussed continuous-time Markov chain models of nucleotide substitution and their application to estimate the distance between two nucleotide sequences. This chapter discusses similar Markov chain models to describe substitutions between amino acids in proteins or between codons in protein-coding genes. It makes straightforward use of the Markov chain theory introduced in Chapter 1, except that the states of the chain are now the 20 amino acids or the 61 sense codons (in the universal genetic code), instead of the four nucleotides. Exercises are provided at the end of the chapter.Less
Chapter 1 discussed continuous-time Markov chain models of nucleotide substitution and their application to estimate the distance between two nucleotide sequences. This chapter discusses similar Markov chain models to describe substitutions between amino acids in proteins or between codons in protein-coding genes. It makes straightforward use of the Markov chain theory introduced in Chapter 1, except that the states of the chain are now the 20 amino acids or the 61 sense codons (in the universal genetic code), instead of the four nucleotides. Exercises are provided at the end of the chapter.
David D. Pollock and Belinda S.W. Chang
- Published in print:
- 2007
- Published Online:
- September 2008
- ISBN:
- 9780199299188
- eISBN:
- 9780191714979
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199299188.003.0008
- Subject:
- Biology, Evolutionary Biology / Genetics
The goal of ancestral inference is to have as accurate a picture of ancestral function as possible. Thus, it is worthwhile to try to understand the nature and cause of the sequence and functional ...
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The goal of ancestral inference is to have as accurate a picture of ancestral function as possible. Thus, it is worthwhile to try to understand the nature and cause of the sequence and functional bias, and how to overcome this bias. This chapter argues that the bias inherent in in the choice to reconstruct the ancestral sequence with the highest posterior probability, along with the optimization bias due to site-specific model inaccuracy, may have biased the frequencies with which certain amino acids are inferred. Amino acids that tend to have consistently low posterior probabilities are most probably undersampled. A simple strategy to address amino acid sampling bias when reconstructing ancestral proteins in the laboratory is discussed.Less
The goal of ancestral inference is to have as accurate a picture of ancestral function as possible. Thus, it is worthwhile to try to understand the nature and cause of the sequence and functional bias, and how to overcome this bias. This chapter argues that the bias inherent in in the choice to reconstruct the ancestral sequence with the highest posterior probability, along with the optimization bias due to site-specific model inaccuracy, may have biased the frequencies with which certain amino acids are inferred. Amino acids that tend to have consistently low posterior probabilities are most probably undersampled. A simple strategy to address amino acid sampling bias when reconstructing ancestral proteins in the laboratory is discussed.
Felicity Savage King and Ann Burgess
- Published in print:
- 1993
- Published Online:
- September 2009
- ISBN:
- 9780192622334
- eISBN:
- 9780191723643
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780192622334.003.0003
- Subject:
- Public Health and Epidemiology, Public Health, Epidemiology
This chapter discusses the importance of proteins. Topics covered include amino acids, complete and incomplete proteins, how the body uses protein, and protein needs. Foods containing protein and how ...
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This chapter discusses the importance of proteins. Topics covered include amino acids, complete and incomplete proteins, how the body uses protein, and protein needs. Foods containing protein and how to calculate protein needs are also described.Less
This chapter discusses the importance of proteins. Topics covered include amino acids, complete and incomplete proteins, how the body uses protein, and protein needs. Foods containing protein and how to calculate protein needs are also described.
PAUL L. HERRLING
- Published in print:
- 1995
- Published Online:
- March 2012
- ISBN:
- 9780192625021
- eISBN:
- 9780191724701
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780192625021.003.0016
- Subject:
- Neuroscience, Molecular and Cellular Systems
Studies on the physiology and pharmacology of excitatory amino acids led to a new understanding of the high degree of complexity of excitatory transmission in the brain, far removed from the early ...
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Studies on the physiology and pharmacology of excitatory amino acids led to a new understanding of the high degree of complexity of excitatory transmission in the brain, far removed from the early concept that post-synaptic depolarization caused excitation and hyperpolarization inhibition. As a consequence of this recent knowledge, workers in the field have proposed therapeutic applications for drugs modulating excitatory amino acid systems, ranging across the entire field of psychiatry and neurology, although only a very limited number of such compounds have reached the stage of clinical evaluation. This chapter attempts to summarize the proposed therapeutic applications for drugs modulating excitatory amino acids and provides a short description of the rationale which led to these proposals. The emphasis is on NMDA-modulating compounds, but there is also mention of possible clinical applications for compounds acting at non-NMDA receptors.Less
Studies on the physiology and pharmacology of excitatory amino acids led to a new understanding of the high degree of complexity of excitatory transmission in the brain, far removed from the early concept that post-synaptic depolarization caused excitation and hyperpolarization inhibition. As a consequence of this recent knowledge, workers in the field have proposed therapeutic applications for drugs modulating excitatory amino acid systems, ranging across the entire field of psychiatry and neurology, although only a very limited number of such compounds have reached the stage of clinical evaluation. This chapter attempts to summarize the proposed therapeutic applications for drugs modulating excitatory amino acids and provides a short description of the rationale which led to these proposals. The emphasis is on NMDA-modulating compounds, but there is also mention of possible clinical applications for compounds acting at non-NMDA receptors.
Irina Ermolina and Yuri Feldman
- Published in print:
- 2015
- Published Online:
- August 2015
- ISBN:
- 9780199686513
- eISBN:
- 9780191766398
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199686513.003.0009
- Subject:
- Physics, Soft Matter / Biological Physics
This chapter presents an overview of the dielectric properties of amino acids and oligopeptides in aqueous solutions. Two relaxation processes identified in the aqueous solutions of amino acids are ...
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This chapter presents an overview of the dielectric properties of amino acids and oligopeptides in aqueous solutions. Two relaxation processes identified in the aqueous solutions of amino acids are ascribed to the molecular motion of the solute and water molecules. The relaxation characteristics (i.e., the dielectric strength and relaxation time) of the process related to amino acids strongly depend on the chemical nature (polar/charged/aromatic) and size of the side groups. The dielectric properties of water are changed by the presence of solute molecules. The relaxation process for water in amino acid solutions becomes wider in comparison with pure water and is well described by the phenomenological Cole–Cole spectral function. A discussion is also presented regarding the effect of molecular mass/length of chain and composition of the polypeptide, the pH of the solution and concentration on the dielectric properties of oligopeptides and polypeptide solutions. Finally, the mechanism of triple-helix-to-single-coil transition in model collagen polypeptides is discussed.Less
This chapter presents an overview of the dielectric properties of amino acids and oligopeptides in aqueous solutions. Two relaxation processes identified in the aqueous solutions of amino acids are ascribed to the molecular motion of the solute and water molecules. The relaxation characteristics (i.e., the dielectric strength and relaxation time) of the process related to amino acids strongly depend on the chemical nature (polar/charged/aromatic) and size of the side groups. The dielectric properties of water are changed by the presence of solute molecules. The relaxation process for water in amino acid solutions becomes wider in comparison with pure water and is well described by the phenomenological Cole–Cole spectral function. A discussion is also presented regarding the effect of molecular mass/length of chain and composition of the polypeptide, the pH of the solution and concentration on the dielectric properties of oligopeptides and polypeptide solutions. Finally, the mechanism of triple-helix-to-single-coil transition in model collagen polypeptides is discussed.
Gina M. Cannarozzi, Adrian Schneider, and Gaston H. Gonnet
- Published in print:
- 2007
- Published Online:
- September 2008
- ISBN:
- 9780199299188
- eISBN:
- 9780191714979
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199299188.003.0005
- Subject:
- Biology, Evolutionary Biology / Genetics
A probabilistic sequence (PS) is a sequence in which each position instead of having a single character (amino acid, nucleotide, or codon), has a vector describing the probability of each symbol ...
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A probabilistic sequence (PS) is a sequence in which each position instead of having a single character (amino acid, nucleotide, or codon), has a vector describing the probability of each symbol being the character at that position. A probabilistic ancestral sequence (PAS) is a reconstructed PS for the common ancestor of several sequences. This chapter presents a formalism to compute the probabilities of each character at each position of the biological sequence for the internal nodes in a given phylogenetic tree using a Markov model of evolution. From this model, the probability of an evolutionary configuration can be computed. In addition, efficient algorithms for computing the likelihood score of aligning a character with a character, a character with a probabilistic character, or two probabilistic characters are derived. These scores can then be used in direct string matching or dynamic programming alignments of probabilistic sequences with insertions and deletions. Applications for these alignments, including long-distance homology searching and multiple sequence alignment construction, are shown.Less
A probabilistic sequence (PS) is a sequence in which each position instead of having a single character (amino acid, nucleotide, or codon), has a vector describing the probability of each symbol being the character at that position. A probabilistic ancestral sequence (PAS) is a reconstructed PS for the common ancestor of several sequences. This chapter presents a formalism to compute the probabilities of each character at each position of the biological sequence for the internal nodes in a given phylogenetic tree using a Markov model of evolution. From this model, the probability of an evolutionary configuration can be computed. In addition, efficient algorithms for computing the likelihood score of aligning a character with a character, a character with a probabilistic character, or two probabilistic characters are derived. These scores can then be used in direct string matching or dynamic programming alignments of probabilistic sequences with insertions and deletions. Applications for these alignments, including long-distance homology searching and multiple sequence alignment construction, are shown.
T. E. SALT
- Published in print:
- 1995
- Published Online:
- March 2012
- ISBN:
- 9780192625021
- eISBN:
- 9780191724701
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780192625021.003.0010
- Subject:
- Neuroscience, Molecular and Cellular Systems
This chapter seeks to review some of the electrophysiological work which has been carried out using excitatory amino acid antagonists. A selection of studies of brain areas has been chosen for review ...
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This chapter seeks to review some of the electrophysiological work which has been carried out using excitatory amino acid antagonists. A selection of studies of brain areas has been chosen for review in an attempt to draw out similarities in receptor function in synaptic transmission: a common feature of these areas is that they have been the subject of intensive study, often using different electrophysiological techniques. A technique which has been widely used in studies of excitatory amino acid synaptic pharmacology, both in vivo and in vitro, is iontophoresis.Less
This chapter seeks to review some of the electrophysiological work which has been carried out using excitatory amino acid antagonists. A selection of studies of brain areas has been chosen for review in an attempt to draw out similarities in receptor function in synaptic transmission: a common feature of these areas is that they have been the subject of intensive study, often using different electrophysiological techniques. A technique which has been widely used in studies of excitatory amino acid synaptic pharmacology, both in vivo and in vitro, is iontophoresis.
Stanley L. Miller and Antonio Lazcano
- Published in print:
- 2002
- Published Online:
- March 2012
- ISBN:
- 9780520233904
- eISBN:
- 9780520928701
- Item type:
- chapter
- Publisher:
- University of California Press
- DOI:
- 10.1525/california/9780520233904.003.0004
- Subject:
- Biology, Evolutionary Biology / Genetics
This chapter focuses on the role of building-block molecules or monomers on the emergence of life. It describes the prebiotic synthesis of amino acids, sugars, purines, and pyrimidines under ...
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This chapter focuses on the role of building-block molecules or monomers on the emergence of life. It describes the prebiotic synthesis of amino acids, sugars, purines, and pyrimidines under conditions relevant to the prebiotic Earth. The formation of amino acids and hydroxy acids was the outcome of a particular set of organic chemical reactions called Strecker-like synthesis that involved aqueous phase interactions among highly reactive intermediates. The results demonstrate that both the amino acids and the hydroxy acids can be synthesized in a simulated primitive ocean even in highly diluted concentrations of hydrogen cyanide (HCN) and aldehyde. The synthesis of sugar-base nucleosides is difficult to achieve under truly prebiotic conditions. Thus, ribose-containing nucleosides are unlikely to have been components of the earliest prebiotic informational macromolecules.Less
This chapter focuses on the role of building-block molecules or monomers on the emergence of life. It describes the prebiotic synthesis of amino acids, sugars, purines, and pyrimidines under conditions relevant to the prebiotic Earth. The formation of amino acids and hydroxy acids was the outcome of a particular set of organic chemical reactions called Strecker-like synthesis that involved aqueous phase interactions among highly reactive intermediates. The results demonstrate that both the amino acids and the hydroxy acids can be synthesized in a simulated primitive ocean even in highly diluted concentrations of hydrogen cyanide (HCN) and aldehyde. The synthesis of sugar-base nucleosides is difficult to achieve under truly prebiotic conditions. Thus, ribose-containing nucleosides are unlikely to have been components of the earliest prebiotic informational macromolecules.
Xun Gu
- Published in print:
- 2010
- Published Online:
- January 2011
- ISBN:
- 9780199213269
- eISBN:
- 9780191594762
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199213269.003.0004
- Subject:
- Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies
As most amino acid substitutions are not related to the functional divergence but only represent the neutral evolution, it becomes crucial how to distinguish statistically between these two ...
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As most amino acid substitutions are not related to the functional divergence but only represent the neutral evolution, it becomes crucial how to distinguish statistically between these two possibilities. Chapter 3 introduced the statistical methods to solve this problem, based on the principle that functional divergence between duplicate genes is highly correlated with the change of evolutionary rate. This chapter discusses several case studies for applying these methods to biological problems.Less
As most amino acid substitutions are not related to the functional divergence but only represent the neutral evolution, it becomes crucial how to distinguish statistically between these two possibilities. Chapter 3 introduced the statistical methods to solve this problem, based on the principle that functional divergence between duplicate genes is highly correlated with the change of evolutionary rate. This chapter discusses several case studies for applying these methods to biological problems.
James P. Ferris
- Published in print:
- 2002
- Published Online:
- March 2012
- ISBN:
- 9780520233904
- eISBN:
- 9780520928701
- Item type:
- chapter
- Publisher:
- University of California Press
- DOI:
- 10.1525/california/9780520233904.003.0005
- Subject:
- Biology, Evolutionary Biology / Genetics
This chapter offers an origin-of-life scenario that requires the prebiotic synthesis of biopolymers. Scientists suggest that that RNA was the most important biopolymer in early (but not necessarily ...
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This chapter offers an origin-of-life scenario that requires the prebiotic synthesis of biopolymers. Scientists suggest that that RNA was the most important biopolymer in early (but not necessarily the first) life on Earth. In this chapter, the possible steps in prebiotic RNA synthesis are examined. Of the various routes thus far explored, RNA synthesis by polymerization of activated monomers has proved the most successful. The chapter also describes the prebiotic synthesis of amino acid polymers or polypeptides. The most productive route to the prebiotic formation of polypeptides in aqueous solution is by means of the N-carboxyanhydride derivatives of their component amino acids.Less
This chapter offers an origin-of-life scenario that requires the prebiotic synthesis of biopolymers. Scientists suggest that that RNA was the most important biopolymer in early (but not necessarily the first) life on Earth. In this chapter, the possible steps in prebiotic RNA synthesis are examined. Of the various routes thus far explored, RNA synthesis by polymerization of activated monomers has proved the most successful. The chapter also describes the prebiotic synthesis of amino acid polymers or polypeptides. The most productive route to the prebiotic formation of polypeptides in aqueous solution is by means of the N-carboxyanhydride derivatives of their component amino acids.
Lawrence E. Hunter
- Published in print:
- 2009
- Published Online:
- August 2013
- ISBN:
- 9780262013055
- eISBN:
- 9780262255288
- Item type:
- chapter
- Publisher:
- The MIT Press
- DOI:
- 10.7551/mitpress/9780262013055.003.0005
- Subject:
- Biology, Biochemistry / Molecular Biology
This chapter discusses biological macromolecules, proteins, and nucleic acids. First, it discusses the chemical structure of proteins, the properties of amino acids that make up most proteins, ...
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This chapter discusses biological macromolecules, proteins, and nucleic acids. First, it discusses the chemical structure of proteins, the properties of amino acids that make up most proteins, protein evolution, and protein function. It then discusses nucleic acids, including the mechanism that directs the synthesis of proteins, the factors that regulate gene expression, and DNA evolution.Less
This chapter discusses biological macromolecules, proteins, and nucleic acids. First, it discusses the chemical structure of proteins, the properties of amino acids that make up most proteins, protein evolution, and protein function. It then discusses nucleic acids, including the mechanism that directs the synthesis of proteins, the factors that regulate gene expression, and DNA evolution.
Ziheng Yang
- Published in print:
- 2014
- Published Online:
- August 2014
- ISBN:
- 9780199602605
- eISBN:
- 9780191782251
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199602605.003.0002
- Subject:
- Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Evolutionary Biology / Genetics
This chapter discusses Markov chain models of amino acid replacement and codon substitution. It then discusses the various methods for estimating the numbers of synonymous and nonsynonymous ...
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This chapter discusses Markov chain models of amino acid replacement and codon substitution. It then discusses the various methods for estimating the numbers of synonymous and nonsynonymous substitutions (dS and dN) between two protein-coding genes. Both the counting and maximum likelihood methods are included.Less
This chapter discusses Markov chain models of amino acid replacement and codon substitution. It then discusses the various methods for estimating the numbers of synonymous and nonsynonymous substitutions (dS and dN) between two protein-coding genes. Both the counting and maximum likelihood methods are included.
Robert Balazs, Richard J. Bridges, and Carl W. Cotman
- Published in print:
- 2005
- Published Online:
- January 2010
- ISBN:
- 9780195150025
- eISBN:
- 9780199865079
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195150025.001.0001
- Subject:
- Neuroscience, Sensory and Motor Systems
This book provides a comprehensive, easy-to-read survey of excitatory amino acids and synaptic transmission. It begins with descriptions of the structure, function, and pharmacology of both the ...
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This book provides a comprehensive, easy-to-read survey of excitatory amino acids and synaptic transmission. It begins with descriptions of the structure, function, and pharmacology of both the ionotropic and the metabotropic glutamate receptors and the glutamate transporters. Subsequent chapters deal with molecular aspects of the regulation of glutamatergic transmission, including receptor trafficking, the role of glutamate transport, the unique molecular architecture of the synapses (post-synaptic density), and the signal transduction pathways mediated by glutamate. Also unique to the book is a chapter on synaptic plasticity that covers long-term potentiation and long-term depression in relationship to synaptic function. It is striking that glutamate is implicated in most of the major neurological diseases, such as stroke, Alzheimer's disease, and schizophrenia.Less
This book provides a comprehensive, easy-to-read survey of excitatory amino acids and synaptic transmission. It begins with descriptions of the structure, function, and pharmacology of both the ionotropic and the metabotropic glutamate receptors and the glutamate transporters. Subsequent chapters deal with molecular aspects of the regulation of glutamatergic transmission, including receptor trafficking, the role of glutamate transport, the unique molecular architecture of the synapses (post-synaptic density), and the signal transduction pathways mediated by glutamate. Also unique to the book is a chapter on synaptic plasticity that covers long-term potentiation and long-term depression in relationship to synaptic function. It is striking that glutamate is implicated in most of the major neurological diseases, such as stroke, Alzheimer's disease, and schizophrenia.
Gary L. Wenk
- Published in print:
- 2010
- Published Online:
- September 2010
- ISBN:
- 9780195388541
- eISBN:
- 9780199863587
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195388541.003.0006
- Subject:
- Neuroscience, Behavioral Neuroscience, Neuroendocrine and Autonomic
Glutamate is an amino acid that your brain uses as a neurotransmitter and it is almost always is excitatory. GABA is also an amino acid that your brain uses as a neurotransmitter and it is almost ...
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Glutamate is an amino acid that your brain uses as a neurotransmitter and it is almost always is excitatory. GABA is also an amino acid that your brain uses as a neurotransmitter and it is almost always inhibitory. These two neurotransmitters are widespread in your brain and tend to compete for turning your neurons on or off. Glutamate makes and breaks connections between neurons; this action allows your brain to learn. For example, if you consume a chemical that blocks the actions of glutamate you become amnestic, unable to remember anything new. The street drugs PCP and ketamine block glutamate receptors and depress the activity of your brain. Your brain makes its own PCP-like neurotransmitter called angeldustin. Chemicals that enhance the action of GABA, such as alcohol, barbiturates, or any of the popular drugs related to Valium and Librium, can make us sleepy, send us into a coma, or kill us by turning off too many neurons in the brain.Less
Glutamate is an amino acid that your brain uses as a neurotransmitter and it is almost always is excitatory. GABA is also an amino acid that your brain uses as a neurotransmitter and it is almost always inhibitory. These two neurotransmitters are widespread in your brain and tend to compete for turning your neurons on or off. Glutamate makes and breaks connections between neurons; this action allows your brain to learn. For example, if you consume a chemical that blocks the actions of glutamate you become amnestic, unable to remember anything new. The street drugs PCP and ketamine block glutamate receptors and depress the activity of your brain. Your brain makes its own PCP-like neurotransmitter called angeldustin. Chemicals that enhance the action of GABA, such as alcohol, barbiturates, or any of the popular drugs related to Valium and Librium, can make us sleepy, send us into a coma, or kill us by turning off too many neurons in the brain.
ROBERT BALÁZS, RICHARD J. BRIDGES, and CARL W. COTMAN
- Published in print:
- 2005
- Published Online:
- January 2010
- ISBN:
- 9780195150025
- eISBN:
- 9780199865079
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195150025.003.0008
- Subject:
- Neuroscience, Sensory and Motor Systems
The ability of glutamate (Glu) to contribute to physiological processes ranging from fast excitatory signaling to synaptic plasticity and neuropathology depends on the considerable diversity that ...
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The ability of glutamate (Glu) to contribute to physiological processes ranging from fast excitatory signaling to synaptic plasticity and neuropathology depends on the considerable diversity that exists among Glu ionotropic and metabotropic receptors. However, it is becoming increasingly apparent that the ability to piece together a picture of the overall functioning of an excitatory amino acid (EAA) synapse also requires a thorough understanding of the mechanisms through which Glu is sequestered in the appropriate cellular compartments and its concentrations regulated. It is within this context that the functional significance of two distinct families of integral membrane transport protein systems has come to be recognized. The excitatory amino acid transporters mediate the uptake of Glu into neurons and glia, whereas the vesicular glutamate transporters are responsible for loading this excitatory transmitter into synaptic vesicles prior to signal-mediated release. The molecular biology and pharmacology of both transporters are discussed.Less
The ability of glutamate (Glu) to contribute to physiological processes ranging from fast excitatory signaling to synaptic plasticity and neuropathology depends on the considerable diversity that exists among Glu ionotropic and metabotropic receptors. However, it is becoming increasingly apparent that the ability to piece together a picture of the overall functioning of an excitatory amino acid (EAA) synapse also requires a thorough understanding of the mechanisms through which Glu is sequestered in the appropriate cellular compartments and its concentrations regulated. It is within this context that the functional significance of two distinct families of integral membrane transport protein systems has come to be recognized. The excitatory amino acid transporters mediate the uptake of Glu into neurons and glia, whereas the vesicular glutamate transporters are responsible for loading this excitatory transmitter into synaptic vesicles prior to signal-mediated release. The molecular biology and pharmacology of both transporters are discussed.
James H. Hunt
- Published in print:
- 2007
- Published Online:
- April 2010
- ISBN:
- 9780195307979
- eISBN:
- 9780199894192
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195307979.003.0006
- Subject:
- Biology, Animal Biology
This chapter argues that many, perhaps most, of the mysteries of hymenopteran sociality might be resolved if investigators would “follow the protein.” It discusses midgut proteases, free amino acids, ...
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This chapter argues that many, perhaps most, of the mysteries of hymenopteran sociality might be resolved if investigators would “follow the protein.” It discusses midgut proteases, free amino acids, fat body and storage protein, polyphenism, and diapause and quiescence.Less
This chapter argues that many, perhaps most, of the mysteries of hymenopteran sociality might be resolved if investigators would “follow the protein.” It discusses midgut proteases, free amino acids, fat body and storage protein, polyphenism, and diapause and quiescence.
