What Is A Base In Biology
basesbase
. Thereof, what is a base in science?
In chemistry, a base is a chemical species that donates electrons, accepts protons, or releases hydroxide ions in aqueous solution. Types of bases include Arrhenius base, Bronsted-Lowry base, and Lewis base.
Subsequently, question is, what is an acid and a base in biology? A solution is a mixture of two or more substances that has the same composition throughout. Some solutions are acids, some are bases. Acids have a higher concentration of hydronium ions than pure water, and a pH lower than 7. Bases have a lower concentration of hydronium ions than pure water, and a pH higher than 7.
Consequently, what is an example of a base in biology?
Examples of bases are sodium hydroxide, calcium carbonate and potassium oxide. A base is a substance that can neutralize the acid by reacting with hydrogen ions. Most bases are minerals that react with acids to form water and salts.
What is pH biology?
PH, quantitative measure of the acidity or basicity of aqueous or other liquid solutions. The term, widely used in chemistry, biology, and agronomy, translates the values of the concentration of the hydrogen ionwhich ordinarily ranges between about 1 and 1014 gram-equivalents per litreinto numbers between 0 and 14.
Phosphodiesters: Alcohols As Nucleophiles In Nucleotidyl Transfers
Phosphodiesters contain two alcohol groups with a bridging phosphoryl group. Two of the four oxygens in the sandwiched phosphoryl group are esterified to those alcohols: hence the terminology of phosphodiesters. Two key biologic classes of phosphodiesters are RNA and DNA molecules. The only covalent bonds holding the RNA nucleoside monophosphate units together and correspondingly the 2deoxyNMP units in DNA chains are the internucleotide phosphodiester bonds . These phosphodiesters span the 3-alcohol of a ribose unit in one NMP or dNMP to the 5-OH of the ribose in the next NMP or dNMP group. All of the three billion dXMP base pairs in the human DNA genomes and the billions of XMP base pairs in all the classes of cellular RNAs are formed enzymatically by nucleotidyl transfer enzymes. Those nucleotidyl transferases, known as RNA polymerases or DNA polymerases, respectively, offer up NTPs or dNTPs for attack at P by the 3-OH of the terminal XMP or dXMP residue in the growing RNA or DNA chain.
Analogously, the activation of each of the 20 proteinogenic amino acids to serve as building blocks in the ribosome-based protein biosynthetic nanomachinery starts with nucleotidyl transfers. All the amino acids are activated as mixed-acyl-AMP anhydrides as the first step in aminoacyl tRNA synthetase active sites . The second step is transfer of the now activated aminoacyl groups to cognate tRNAs to be ferried to the ribosomes by chaperone proteins.
The Structure Of This Book
The volume begins with this introductory chapter then proceeds to the chemical properties of inorganic phosphate that enable its several biological roles. The dimeric phosphoric anhydride inorganic pyrophosphate is then addressed as the central functional group that enables the POP anhydride linkage to function throughout biology via the dual properties of thermodynamic activation coupled to kinetic stability in aqueous medial at physiological pH values.
From inorganic pyrophosphate with one POP anhydride bond it is a short chemical traverse to ATP with two POP anhydride bonds in its kinetically stable tetra-anionic triphosphate side chain. Adenine may have been available prebiotically from condensation of HCN and AMP from phosphoribosylation. AMP-binding proteins may have evolved early to give AMP and then ADP and ATP pride of place in phosphoric anhydride energy metabolism.
The two POP anhydrides in ATP and other NTPs and 2deoxyNTPs offer nucleophiles three choices of electrophilic phosphorus atoms to attack. Transfer of P as the PO32 group opens the biological world of phosphate monoesters brought about by phosphoryl transfer enzymes and includes all the kinases for low molecular weight metabolites and for proteins in their myriads.
The last part on low molecular weight phosphate metabolites examines the occurrence and biological consequences of replacement of one of the four oxygens of phosphate by carbon, nitrogen, or sulfur atoms.
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Proftalk: Beards Biology And Media Psychology Oh My
Posted on November 10, 2021 at 4:54 PM, updated November 10, 2021 at 4:54 PM
Each week, Cleveland State University will profile new faculty members with a getting to know you feature called ProfTALK. Learn about your profs background, bona fides and how they contribute to the momentum of Engaged Learning. Then get behind the desk and learn a little more about what makes them tick. This week, we dive into biology and beards to movies and media psychology! Meet John Van Stan II, Ph.D., and Yuchen Liu, Ph.D.!
Biological, Geological and Environmental Sciences Associate Professor John T. Van Stan II, Ph.D.
Ph.D., Geography, University of Delaware
M.S., Geography, University of Delaware
M.S., Environmental Science and Policy, Johns Hopkins University
B.A., English Literature, University of Delaware
B.S., Environmental Science, University of Delaware
What three words come to mind when you think of Cleveland State University?
Lakeside, Snow, Viking.
Phosphomonoesters: Alcohols As Nucleophiles In Phosphoryl Transfers
After consideration of the metabolic changes enabled by the thermodynamically activated phosphorylated frameworks, just noted, we turn to phosphate esters. Most discussions of biological phosphates would start with phosphomonoesterse.g. glucose-6-phosphateand then phosphodiesterse.g. the 35-internucleotide phosphodiester bonds in RNA and DNAincluding their routes of formation and breakdown.
Indeed, the capture of phosphoryl groups by alcohol functionalities in cosubstrates dominates sugar metabolism. We believe strongly that a prior discussion of phosphoric anhydride chemical biology then gives the insights necessary to understand how ATP is a phosphorylating reagent for alcohol groups in the above metabolites. This is the essence of the strategy of over 100 low molecular weight kinase enzymes and more than 500 protein kinases in humans.
Phosphomonoester metabolites turn over in a dynamic fashion. The catalyzed hydrolysis of phosphomonoesters back to alcohol and inorganic phosphate are the province of phosphatase enzymes. These include low molecular weight selective phosphatases as well as many kinds of phosphoprotein phosphatases.
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A Message From The Department Chair
Isabelle Deschenes, PhDWelcome to The Ohio State University Department of Physiology and Cell Biology!Faculty members in the Department are involved in cutting-edge research embracing Physiology and Cell Biology in the context of diseases. Our research spans a continuum from basic to translational research with strong programs in cardiovascular, skeletal muscle, pulmonary, and cancer biology research. Our quickly growing department is a stimulating environment for faculty to mentor graduate, undergraduate and medical students along with post-doctoral fellows in acquiring the skills they need to develop as leaders in academia, medical professions or in the biotechnology and biopharmaceutical industries. We strive to provide a collegial, collaborative and diverse environment with extensive synergy between our Department and faculty in the College of Medicine but also in other colleges such as Pharmacy, Veterinary Medicine, Nursing, Dentistry and Arts and Sciences. Together, faculty, students and staff, capitalize on the rich environment provided at The Ohio State University to increase our knowledge of the human body to develop novel diagnosis and therapies.Thank you for visiting our website and exploring our research and educational programs.
As A Nucleophilic Reagent
The hydroxide ion is intermediate in nucleophilicity between the fluoride ion F, and the amide ion NH2. The hydrolysis of an ester
- R1COR2 + H2O R1COH + HOR2
also known as saponification is an example of a nucleophilic acyl substitution with the hydroxide ion acting as a nucleophile. In this case the leaving group is an alkoxide ion, which immediately removes a proton from a water molecule to form an alcohol. In the manufacture of soap, sodium chloride is added to salt out the sodium salt of the carboxylic acid this is an example of the application of the common ion effect.
Other cases where hydroxide can act as a nucleophilic reagent are amide hydrolysis, the Cannizzaro reaction, nucleophilic aliphatic substitution, nucleophilic aromatic substitution, and in elimination reactions. The reaction medium for KOH and NaOH is usually water but with a phase-transfer catalyst the hydroxide anion can be shuttled into an organic solvent as well, for example in the generation of the reactive intermediate dichlorocarbene.
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Families Of Thermodynamically Activated Phosphoryl Derivatives
While phosphoric anhydride linkages in nucleoside triphosphates are the central phosphoryl group transfer currency in cells, other phosphoryl functional groups are also thermodynamically activated and sufficiently kinetically stable to serve as phosphoryl group donors.10 Three of them are doubly activated for both phosphoryl group transfer and transfer of the other moiety as an activated electrophile. The classes of metabolites are mixed sulfuricphosphoric anhydrides, represented by 3-phospho-5-adenosine phosphosulfate , acyl phosphates such as the simple acetyl phosphate, and phosphorylated enols of which phosphoenolpyruvate is the paradigm .
All three can be attacked by one of the terminal oxyanions of ADP in the presence of particular enzyme catalysts to make ATP, thus evincing phosphoryl group potential. More usefully, PAPS is the cellular donor of the activated sulfuryl group to oxygen and nitrogen cosubstrate nucleophiles. Acyl phosphates are donors of activated acyl groups in a variety of cellular acyl transferase active sites. While phosphoenolpyruvate is thought of mainly as a phosphoryl group donor, the enolpyruvyl group is transferred intact in bacterial assembly of aromatic scaffolds and in cell wall peptidoglycan construction.
Chemical Biology Of Phosphorus
Inorganic phosphate, typically as fluorapatite or hydroxyapatite , in limestone and mudstone rocks can vary from 4 to 30% in those rocks.5 That abundance, coupled with the observation that over 99% of phosphorus biology occurs in the P= oxidation state, makes inorganic phosphate and its compounds the center of phosphorus chemical biology. Throughout this volume, we take the simplifying view that the chemistry of inorganic phosphate, its anhydrides, monoesters and diesters with alcohol groups of metabolites, both of low molecular weight and as macromolecules, dominate and determine the myriad roles of phosphate in biology .
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Why Is Hydroxide Written As Oh
Its written in reverse order because hydroxide is a polyatomic ion that still needs balance to be part of a compound. In most cases, when OH bonds to another ion the oxygen is the one that bonds to the other ion. Because of this its is written as OH, so that it will be easier to tell how the molecule is bonded.
Title: From Logic To Biology Via Physics: A Survey
Abstract: This short text summarizes the work in biology proposed in our book,Perspectives on Organisms, where we analyse the unity proper to organisms bylooking at it from different viewpoints. We discuss the theoretical roles ofbiological time, complexity, theoretical symmetries, singularities and criticaltransitions. We explicitly borrow from the conclusions in some key chapters andintroduce them by a reflection on “incompleteness”, also proposed in the book.We consider that incompleteness is a fundamental notion to understand the wayin which we construct knowledge. Then we will introduce an approach tobiological dynamics where randomness is central to the theoreticaldetermination: randomness does not oppose biological stability but contributesto it by variability, adaptation, and diversity. Then, evolutionary andontogenetic trajectories are continual changes of coherence structuresinvolving symmetry changes within an ever-changing global stability.
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What Is Biology At Ntnu
The word biology is derived from the greek words /bios/ meaning /life/ and /logos/ meaning /study/ and is defined as the science of life and living organisms. An organism is a living entity consisting of one cell e.g. bacteria, or several cells e.g. animals, plants and fungi.
Aspects of biological science range from the study of molecular mechanisms in cells, to the classification and behaviour of organisms, how species evolve and interaction between ecosystems.
Biology often overlaps with other sciences for example, biochemistry and toxicology with biology, chemistry, and medicine biophysics with biology and physics stratigraphy with biology and geography astrobiology with biology and astronomy. Social sciences such as geography, philosophy, psychology and sociology can also interact with biology, for example, in administration of biological resources, developmental biology, biogeography, evolutionary psychology and ethics.
Basic Salts Containing Hydroxide
In some cases the products of partial hydrolysis of metal ion, described above, can be found in crystalline compounds. A striking example is found with zirconium. Because of the high oxidation state, salts of Zr4+ are extensively hydrolyzed in water even at low pH. The compound originally formulated as ZrOCl2·8H2O was found to be the chloride salt of a tetrameric cation 8+ in which there is a square of Zr4+ ions with two hydroxide groups bridging between Zr atoms on each side of the square and with four water molecules attached to each Zr atom.
The mineral malachite is a typical example of a basic carbonate. The formula, Cu2CO32 shows that it is halfway between copper carbonate and copper hydroxide. Indeed, in the past the formula was written as CuCO3·Cu2. The crystal structure is made up of copper, carbonate and hydroxide ions. The mineral atacamite is an example of a basic chloride. It has the formula, Cu2Cl3. In this case the composition is nearer to that of the hydroxide than that of the chloride CuCl2·3Cu2. Copper forms hydroxyphosphate , arsenate , sulfate , and nitrate compounds. White lead is a basic lead carbonate, 2·Pb2, which has been used as a white pigment because of its opaque quality, though its use is now restricted because it can be a source for lead poisoning.
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Structure Begets Enzymatic Activity
The increased stability of RNA duplexes allows for highly diverse secondary and tertiary structures including triplexes, pseudoknots, loops, and junctions. This array of potential secondary and tertiary structures enable RNA to fold into enzymatically active molecules such as RNAse P, which cleave tRNA to their mature length. Artificial ribozymes have also been developed in labs with an array of functionality including self replication. RNA is so versatile that it is widely believed that in early life, before DNA and proteins, RNA alone performed both information storage and catalytic functions, establishing lifes singular dependence on nucleic acids.
Following the removal of the 2 OH protecting group in post-synthesis processing, a new vulnerability begins. RNA is susceptible to alkaline hydrolysis which cleaves the backbone at the phosphodiester bond. These combined factors make the manufacture of RNA unique and contribute to differences between RNA and DNA in pricing and availability of both modifications and oligo lengths.
Compared to DNA, the unique manufacturing process required with RNA further demonstrates the significant impact of RNAs 2 OH group, which is also seen in nature. Expanded interest and study concerning RNAs central role in biology has spurred innovation in RNA synthesis, and the two fields of RNA research and RNA synthesis will continue to advance in conjunction with each other, both with a focus on RNAs dynamic 2 OH.
What State Does Oh Stand For
Ohio, Buckeye State, OH a midwestern state in north central United States in the Great Lakes region.
What is the difference between OH and HO?
Here is the difference Between OH and HO: HO is a molecule containing positive Hydrogen Oxygen atoms i.e it is a cation. OH is a molecule containing negative Hydrogen Oxygen atoms i.e it is an anion. Both are ions, HO+ is Hydroxide, OH is Oxyhydride.
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The Element: Discovery Abundance Valence States
Adult humans contain about 2 pounds of phosphorus, almost exclusively in the form of the fully oxidized phosphate atoms. Some 85% is deposited in bones and teeth as calcium phosphate in the form of crystalline hydroxyapatite. The remainder is in soft tissues, with the serum concentration of soluble inorganic phosphate maintained within narrow limits at 1.1 to 1.4 mM. At these levels, phosphorus is slightly less abundant than calcium, and about half the levels of bodily nitrogen . The other three abundant elements H, C, and O come in at 7 kg, 16 kg, and 43 kg, respectively. The 1% abundance of phosphorus by mass belies the essential roles of phosphates. Lord Alexander Todd, British chemist and Nobelist who carried out the first syntheses of nucleotides, remarked Where there is life, there is phosphorus.1
Phosphorus sits just below nitrogen in the periodic table, as atomic number 15, with a molecular weight of 30.974 atomic mass units. While 31P is the most abundant and stable isotope, the short lived radioactive 32P has found extensive use in radiotracer studies and the stable heavy atom isotope 33P also has its uses as a tracer for phosphorus metabolism.
KK
Phosphonates Phosphoramidates And Phosphorothioates
There are three additional classes of naturally occurring phosphate derivatives that reflect substitution of one of the four phosphate group oxygens by a carbon, a nitrogen, or a sulfur atom. , yielding phosphonate, phosphoramidate, or phosphorothioate scaffolds, respectively.12
There are some 200 known microbial metabolites with the direct CP bonds.13 The CP links are chemically stable to hydrolysis, resistant to phosphatase action, and offer producers a strategy for generating stable molecules in hostile microenvironments and for the formation of antimetabolites as molecular weaponry. There is a single enzymatic route for CP bond formation in biology, the enzyme PEP mutase, converting the enol phosphate PEP to the CP direct linkage in phosphonopyruvate. This is the gateway enzyme to all downstream CP metabolites, including some very rare phosphinates with two CP bonds and two OP bonds .
The NPO32 linkage is termed a phosphoramidate. There are only about 50 known phosphoramidate metabolites. They show up mainly in three distinct categories. Five of the twenty proteinogenic amino acids are known to undergo enzymatic N-phosphorylations on the way to end product metabolites, including phosphoramidate linkages in the capsular polysaccharide of some strains of the human gastrointestinal pathogen Camphylobacter jejuni.14
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