msb200922-sup
... metabolism and transport of tyrosine (tyr). Circular nodes represent metabolites and edges represent biochemical reactions. For simplicity, only abbreviations of metabolite names and enzyme E.C. (Enzyme Commission) numbers are specified (explicit names are given in Supp. Table 2). Metabolites marked ...
... metabolism and transport of tyrosine (tyr). Circular nodes represent metabolites and edges represent biochemical reactions. For simplicity, only abbreviations of metabolite names and enzyme E.C. (Enzyme Commission) numbers are specified (explicit names are given in Supp. Table 2). Metabolites marked ...
Chapter 4
... presence of catalysts, favorable temperature, and presence of substrates are maintained. As a given enzyme can both synthesize and degrade, both processes will continue even at equilibrium. D is incorrect because at equilibrium there is no net change in amounts, but it is not necessary for concentra ...
... presence of catalysts, favorable temperature, and presence of substrates are maintained. As a given enzyme can both synthesize and degrade, both processes will continue even at equilibrium. D is incorrect because at equilibrium there is no net change in amounts, but it is not necessary for concentra ...
+ H 2 O(g)
... • Often hard to predict products unless the substance breaks into its ionic components (or memorize some basic types of reactions) • Often are the cause of explosions ...
... • Often hard to predict products unless the substance breaks into its ionic components (or memorize some basic types of reactions) • Often are the cause of explosions ...
Types of Reactions
... If you can’t come to the Monday Re-Do session, you MUST come before school two days for help. You MUST let me know that you’re interested by Thursday!!!! ...
... If you can’t come to the Monday Re-Do session, you MUST come before school two days for help. You MUST let me know that you’re interested by Thursday!!!! ...
Clustering Gene Expression Data
... • genetic interactions • interactions automatically extracted from the scientific literature • adapting approach to RNAi screens in mammalian cells • more genes • lower density of known interactions • more uncertainty in measurements • devising methods that use these models to determine which follow ...
... • genetic interactions • interactions automatically extracted from the scientific literature • adapting approach to RNAi screens in mammalian cells • more genes • lower density of known interactions • more uncertainty in measurements • devising methods that use these models to determine which follow ...
The RAVEN Toolbox and Its Use for Generating a Genome
... files to generate a GEM representing a metabolic network across all of the species annotated in KEGG, i.e. this would lead to a network comprising 7029 metabolites, 8398 reactions and 843369 genes, when using the most current version of the KEGG database. A GEM for the organism of interest is then c ...
... files to generate a GEM representing a metabolic network across all of the species annotated in KEGG, i.e. this would lead to a network comprising 7029 metabolites, 8398 reactions and 843369 genes, when using the most current version of the KEGG database. A GEM for the organism of interest is then c ...
ProdoNet: identification and visualization of prokaryotic gene
... A variety of databases supply valuable information on transcription factor binding sites and gene regulation. For prokaryotes, these include databases that focus on a single model organism, as RegulonDB for Escherichia coli (1) or DBTBS for Bacillus subtilis (2). Others cover a range of species, lik ...
... A variety of databases supply valuable information on transcription factor binding sites and gene regulation. For prokaryotes, these include databases that focus on a single model organism, as RegulonDB for Escherichia coli (1) or DBTBS for Bacillus subtilis (2). Others cover a range of species, lik ...
Genome-wide association studies for microbial genomes
... Phage packaging machinery Bacteriophage P4 cluster R1t-like Streptococcal phages Phage family Inoviridae Integrons CBSS.350688.3.peg.1509 Potassium homeostasis Phenazine biosynthesis Cyanophage Outer membrane proteins Importance → ...
... Phage packaging machinery Bacteriophage P4 cluster R1t-like Streptococcal phages Phage family Inoviridae Integrons CBSS.350688.3.peg.1509 Potassium homeostasis Phenazine biosynthesis Cyanophage Outer membrane proteins Importance → ...
As Powerpoint Slide
... Metabolic engineering based on systems biology for chemicals production Jianzhong LIU 1, 2 ;Zhiming WENG 1 ;Yue WANG 1 ;Hui CHAO 2 ;Zongwan MAO 2 ; ...
... Metabolic engineering based on systems biology for chemicals production Jianzhong LIU 1, 2 ;Zhiming WENG 1 ;Yue WANG 1 ;Hui CHAO 2 ;Zongwan MAO 2 ; ...
ch 40: an introduction to animal structure and function
... stomach and not stressed and at a specific temperature (must use a specific temp since their body temperature and metabolic rate change over time depending on environmental temperature *any form of activity (ex. writing/turning head) will increase the metabolic rate over the BMR or SMR C. metabolic ...
... stomach and not stressed and at a specific temperature (must use a specific temp since their body temperature and metabolic rate change over time depending on environmental temperature *any form of activity (ex. writing/turning head) will increase the metabolic rate over the BMR or SMR C. metabolic ...
Connections of Carbohydrate, Protein, and Lipid
... You have learned about the catabolism of glucose, which provides energy to living cells. But living things consume more than glucose for food. ...
... You have learned about the catabolism of glucose, which provides energy to living cells. But living things consume more than glucose for food. ...
Gas Exchange
... oxygen. In some, such as nemertean worms a circulatory system exists that functions to carry nutrients from the gut to other tissues. • Larger organisms and organisms living in low oxygen environments have evolved such structures and circulatory systems. The diffusion of O2 across such surfaces is m ...
... oxygen. In some, such as nemertean worms a circulatory system exists that functions to carry nutrients from the gut to other tissues. • Larger organisms and organisms living in low oxygen environments have evolved such structures and circulatory systems. The diffusion of O2 across such surfaces is m ...
Multiple Knockout Analysis of Genetic Robustness in the Yeast
... Using exhaustive multiple knockouts search we found 48 essential genes, 16 essential pairs, 16 triplets, and 38 essential quadruples, overall involving 157 contributing genes. The gene knockout sampling method identified an additional 174 contributing genes with k-robustness levels greater than four ...
... Using exhaustive multiple knockouts search we found 48 essential genes, 16 essential pairs, 16 triplets, and 38 essential quadruples, overall involving 157 contributing genes. The gene knockout sampling method identified an additional 174 contributing genes with k-robustness levels greater than four ...
Chapter 5: Microbial Metabolism
... Chapter 5: Microbial Metabolism Below you will find answers to the "Review" study questions found at the end of this chapter in Microbiology: An Introduction, 7th edition. 1. Metabolism is the sum of all chemical reactions that occur within a living organism. 2. Catabolic reactions break down organi ...
... Chapter 5: Microbial Metabolism Below you will find answers to the "Review" study questions found at the end of this chapter in Microbiology: An Introduction, 7th edition. 1. Metabolism is the sum of all chemical reactions that occur within a living organism. 2. Catabolic reactions break down organi ...
overview-omics - SRI International
... Typically a time course, but does not have to be Need to tell Pathway Tools which columns to use Same output color / cutoff selections as single experiment If you use automatic color scale, it’s set to the maximum shift in the experiment Thus, all time points / data sets comparable A goo ...
... Typically a time course, but does not have to be Need to tell Pathway Tools which columns to use Same output color / cutoff selections as single experiment If you use automatic color scale, it’s set to the maximum shift in the experiment Thus, all time points / data sets comparable A goo ...
Chapter 8: An Introduction to Metabolism
... b. lost as heat because of the second law of thermodynamics (149) 14. An endergonic reaction could be described as one that will b. produce products with more free energy than the reactants (146) 15. What is most directly responsible for the specificity of a protein enzyme? e. the R groups of the am ...
... b. lost as heat because of the second law of thermodynamics (149) 14. An endergonic reaction could be described as one that will b. produce products with more free energy than the reactants (146) 15. What is most directly responsible for the specificity of a protein enzyme? e. the R groups of the am ...
The Impact of Non-Enzymatic Reactions and Enzyme Promiscuity on
... or toxic chemicals, or biotic interactions with other species. These stress situations can manifest as an acute pulse, or be sustained over time, and can affect cellular functioning and ultimately impair cell growth, replicative capabilities, and/or promote aging. Stress-induced damage to biological ...
... or toxic chemicals, or biotic interactions with other species. These stress situations can manifest as an acute pulse, or be sustained over time, and can affect cellular functioning and ultimately impair cell growth, replicative capabilities, and/or promote aging. Stress-induced damage to biological ...
Principles of Enzyme Catalysis\Principles of Enzyme Catalysis.wpd
... A. Catalysts rely on kinetic rather than thermodynamic factors. A catalyst acts by increasing the rate of a chemical reaction without being consumed in the process. Therefore, a single catalyst molecule can participate in multiple reaction cycles. The rate, or more correctly the rate constant, of th ...
... A. Catalysts rely on kinetic rather than thermodynamic factors. A catalyst acts by increasing the rate of a chemical reaction without being consumed in the process. Therefore, a single catalyst molecule can participate in multiple reaction cycles. The rate, or more correctly the rate constant, of th ...
Microbiology: A Systems Approach, 2nd ed.
... use only the glycolysis scheme to incompletely oxidize glucose – Aerobic respiration: When oxygen is used as the final electron acceptor at the end of the respiration scheme to produce H2O. – Anaerobic respiration: Does not use molecular oxygen as the final electron acceptor, but uses nitrogen or co ...
... use only the glycolysis scheme to incompletely oxidize glucose – Aerobic respiration: When oxygen is used as the final electron acceptor at the end of the respiration scheme to produce H2O. – Anaerobic respiration: Does not use molecular oxygen as the final electron acceptor, but uses nitrogen or co ...
Nerve activates contraction
... (movement), Transport (of macromolecules into and out of cells), and Chemical Work (drive endergonic reactions in anabolic pathways) Plants transform light to chemical energy; they do not produce energy. ...
... (movement), Transport (of macromolecules into and out of cells), and Chemical Work (drive endergonic reactions in anabolic pathways) Plants transform light to chemical energy; they do not produce energy. ...
Toxicant Disposition and Metabolism
... • Most significant of all toxicant oxidation reactions. • Adds one atom of molecular oxygen to substrate, other atom becomes a reactive oxygen species (with potential for oxidative damage within the cell). • Very important in detoxication of many toxicants. • Most important for bioactivations: ...
... • Most significant of all toxicant oxidation reactions. • Adds one atom of molecular oxygen to substrate, other atom becomes a reactive oxygen species (with potential for oxidative damage within the cell). • Very important in detoxication of many toxicants. • Most important for bioactivations: ...
Regulation of metabolic pathways at the cellular level
... • Proteinkinases and phosphatases • Phosphorylation can activate or inhibit • Fast switching between active and inactive form of the enzyme ...
... • Proteinkinases and phosphatases • Phosphorylation can activate or inhibit • Fast switching between active and inactive form of the enzyme ...
Metabolic network modelling
Metabolic network reconstruction and simulation allows for an in-depth insight into the molecular mechanisms of a particular organism. In particular, these models correlate the genome with molecular physiology. A reconstruction breaks down metabolic pathways (such as glycolysis and the Citric acid cycle) into their respective reactions and enzymes, and analyzes them within the perspective of the entire network. In simplified terms, a reconstruction collects all of the relevant metabolic information of an organism and compiles it in a mathematical model. Validation and analysis of reconstructions can allow identification of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. This knowledge can then be applied to create novel biotechnology.In general, the process to build a reconstruction is as follows: Draft a reconstruction Refine the model Convert model into a mathematical/computational representation Evaluate and debug model through experimentation↑