Life and Its Chemical Foundations

2019 ◽  
pp. 19-55
Keyword(s):  
Chemical Reactions ◽  
Chemical Bonds ◽  
Complex Molecules ◽  
Minor Elements ◽  
Large Complex ◽  
Metabolic Reactions ◽  
Living Organisms ◽  
Life On Earth ◽  
Long Chains

This chapter focuses on the chemical foundations of life. Matter is made up of elements classified into major and minor elements. Elements are made up of atoms which in turn are made up of sub-atomic particles called protons, electrons and neutrons. Chemical bonds are unions of electron structures when atoms lose, gain or share one or more electrons with other atoms. Water is important to life and has unique properties making it ideal to life on Earth. The pH of a substance is a measure of the balance between H+ and OH- ions ranging from 0 to 14 on a log scale. Most metabolic reactions that maintain life occur in living organisms involve five types of chemical reactions. Macromolecules are large complex molecules made up of repeating units (monomers) of sometimes the same molecule or of different molecules joined together by chemical bonds to form very long chains (polymers).

4. The burning issue: molecules and energy

2003 ◽  
pp. 70-93
Author(s):  
Philip Ball
Keyword(s):  
Citric Acid ◽  
Chemical Reactions ◽  
Citric Acid Cycle ◽  
Living Cells ◽  
Metabolic Processes ◽  
Acid Cycle ◽  
Cellular Life ◽  
Metabolic Reactions ◽  
Molecular Reactions ◽  
Living Organisms

‘The burning issue: molecules and energy’ describes how energy can be transferred through molecular reactions. Metabolic processes are the foundation of cellular life. All chemical reactions increase entropy (or disorder), but living cells maintain their order by carefully controlling metabolic reactions. In living organisms glucose is broken down into pyruvate through glycolysis. Pyruvate then enters the citric acid cycle, which is a series of reactions that generate electrons which generate ATP — the cell's ‘fuel’. Many scientists, most notably Alfred Nobel, have sought to develop molecules which contain huge amounts of energy safely. These molecules can be used to build civilization — or destroy life.

Proteins Perform Multiple Functions: Enzymes, Receptors, Ion Channel Proteins

2014 ◽  
Author(s):  
Eugene H. Cordes
Keyword(s):  
Ion Channel ◽  
Chemical Reactions ◽  
Chemical Reaction ◽  
Information Transfer ◽  
Protein Structures ◽  
Chemical Bonds ◽  
Channel Proteins ◽  
Ion Channel Proteins ◽  
Age Of The Universe ◽  
Living Organisms

As emphasized in the preceding chapter, there are an unimaginably large number of possible protein structures based on the sequence of amino acids along the amino acid chain. Through the process of evolution, nature has chosen a minute fraction of them to create proteins that provide for the necessities of life. Among all the functions that proteins serve in living organisms, I focus on the three that relate most directly to my tales of drug discovery: catalysis, information transfer, and control of the intracellular milieu. These functions are served by, respectively, enzymes, receptors, and ion channel proteins. I spend most of the time discussing enzymes, because most of the stories in the later chapters focus on enzymes. There are occasions when I refer to receptors and ion channels, as well, but because enzymes are the stars of the stories, let’s start there. Chemical reactions are processes during which one or more molecules are converted into different ones. Chemical reactions involve breaking and forming of the chemical bonds that hold atoms together in molecules. Certain chemical bonds in the starting molecules (the reactants) are broken, followed by the formation of new ones, leading to the end products. All the atoms in the reactants are found in the products; they are just rearranged. A simple example is provided by diamond and graphite. Diamond is brilliant and the hardest natural substance known; graphite is black and very soft. Yet, both diamond and graphite are composed entirely of carbon atoms. The carbon atoms are linked differently by the chemical bonds holding them together, yielding substances with very different properties. It may surprise you to know that graphite is actually very slightly more stable than diamond. So if we wait long enough, the chemical reaction . . . Diamond → Graphite . . . might be expected to occur. However, do not search for evidence of black dots in your wedding diamond. This may be the slowest chemical reaction of all and may take longer than the age of the universe to get anywhere.

scholarly journals Artificial Biosynthetic Pathway for an Unnatural Terpenoid with an Iridiumcontaining P450

2020 ◽  
Author(s):  
Jing Huang ◽  
Zhennan Liu ◽  
brandon bloomer ◽  
Douglas Clark ◽  
Aindrila Mukhopadhyay ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Synthetic Biology ◽  
Chemical Reactions ◽  
Biosynthetic Pathway ◽  
Metabolic Networks ◽  
Complex Molecules ◽  
Whole Cells ◽  
Porphyrin Complex ◽  
Heme Transport ◽  
Artificial Metalloenzymes

<div>Synthetic biology enables microbial hosts to produce complex molecules that are</div><div>otherwise produced by organisms that are rare or difficult to cultivate, but the structures of these</div><div>molecules are limited to chemical reactions catalyzed by natural enzymes. The integration of</div><div>artificial metalloenzymes (ArMs) that catalyze abiotic reactions into metabolic networks could</div><div>broaden the cache of molecules produced biosynthetically by microorgansms. We report the</div><div>assembly of an ArM containing an iridium-porphyrin complex in the cytoplasm of a terpene</div><div>producing Escherichia coli by a heterologous heme transport machinery, and insertion of this ArM</div><div>into a natural biosynthetic pathway to produce an unnatural terpenoid. This work shows that</div><div>synthetic biology and synthetic chemistry, incorporated together in whole cells, can produce</div><div>molecules previously inaccessible to nature.</div>

scholarly journals The Principle of Conservation of Structural Aspect: Facilitating Visual Communication and Learning in Organic Chemistry Instruction

2019 ◽  
Author(s):  
john andraos
Keyword(s):  
Organic Chemistry ◽  
Chemical Reactions ◽  
Reaction Mechanisms ◽  
Visual Communication ◽  
Structural Aspect ◽  
Chemical Bonds ◽  
Journal Articles ◽  
Chemistry Instruction ◽  
Individual Reaction ◽  
Training Exercises

<p>An effective pedagogical method is presented for the visual communication of chemical reactions learned in organic chemistry undergraduate courses. The basis for the method is the preservation of the visual aspect of reactant and product structures so that the tracking of cleaved and formed chemical bonds is made self-evident. This consequently leads to improved clarity of presentation and a better understanding and grasp of proposed reaction mechanisms to explain product outcomes. The method is demonstrated for a variety of individual reaction types and synthesis plans. Various visual training exercises are also presented using ChemDraw Ultra 7.0 software and literature table of contents (TOC) graphics appearing in journal articles.</p><br>

Sources of Air Pollution

2018 ◽  
pp. 220-258
Author(s):  
Abderrezak Khelfi
Keyword(s):  
Air Pollution ◽  
Particulate Matter ◽  
Adverse Effects ◽  
Chemical Reactions ◽  
Dust Storms ◽  
Pollution Sources ◽  
Atmospheric Gases ◽  
Secondary Pollutants ◽  
Harmful Substances ◽  
Life On Earth

This chapter describes how air is a complex natural gaseous system essential to support life on Earth. Air pollution comes from a wide variety of sources, which discharge of harmful substances into the atmosphere, causing adverse effects to humans and the environment. They can be natural or anthropogenic. Natural air pollution sources are multiple and include volcanic eruption, fire, ocean vapors, dust storms and fermentation of organic materials. However, the range and quantities of chemicals discharged into the atmosphere from industry, transport, agriculture, energy production, domestic heating, and many other human activities, have increased dramatically. Some pollutants are emitted directly into the atmosphere and are known as primary pollutants (NOx, SOx, particulate matter, etc.). Others are formed in the air as a result of chemical reactions with other pollutants and atmospheric gases; these are known as secondary pollutants like ozone. This chapter provides an overview on air pollution sources as well as the ways in which pollutants can affect human health and the environment.

scholarly journals Sensing the allosteric force

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Olga Bozovic ◽  
Brankica Jankovic ◽  
Peter Hamm
Keyword(s):  
Ligand Binding ◽  
Binding Affinity ◽  
Chemical Reactions ◽  
Peptide Ligand ◽  
Allosteric Site ◽  
Small Peptide ◽  
Changing Environment ◽  
Allosteric Communication ◽  
Signalling Cascades ◽  
Living Organisms

AbstractAllosteric regulation is an innate control in most metabolic and signalling cascades that enables living organisms to adapt to the changing environment by tuning the affinity and regulating the activity of target proteins. For a microscopic understanding of this process, a protein system has been designed in such a way that allosteric communication between the binding and allosteric site can be observed in both directions. To that end, an azobenzene-derived photoswitch has been linked to the α3-helix of the PDZ3 domain, arguably the smallest allosteric protein with a clearly identifiable binding and allosteric site. Photo-induced trans-to-cis isomerisation of the photoswitch increases the binding affinity of a small peptide ligand to the protein up to 120-fold, depending on temperature. At the same time, ligand binding speeds up the thermal cis-to-trans back-isomerisation rate of the photoswitch. Based on the energetics of the four states of the system (cis vs trans and ligand-bound vs free), the concept of an allosteric force is introduced, which can be used to drive chemical reactions.

scholarly journals Role of Water for Life

2019 ◽  
Vol 03 (01) ◽  
pp. 3-19
Author(s):  
Bengt Nordén
Keyword(s):  
Chemical Potential ◽  
Genetic Recombination ◽  
Solar Systems ◽  
Gene Recognition ◽  
Low Dielectric ◽  
Sexual Recombination ◽  
Dna Strand Exchange ◽  
Living Organisms ◽  
Dna Strand ◽  
Life On Earth

The behavior of benzoic acid in polyethylene inspired me to reflect on why water is a unique molecule that all living organisms depend upon. From properties of DNA in aqueous solution a seemingly counter-intuitive conjecture emerges: water is needed for the creation of certain dry low-dielectric nm-size environments where hydrogen bonding exerts strong recognition power. Such environments seem to be functionally crucial, and their interactions with other hydrophobic environments, or with hydrophobic agents that modulate the chemical potential of water, can cause structural transformations via ‘hydrophobic catalysis’. Possibly combined with an excluded volume osmosis effect (EVO), hydrophobic catalysis may have important biological roles, e.g., in genetic recombination. Hydrophobic agents are found to strongly accelerate spontaneous DNA strand exchange as well as certain other DNA rearrangement reactions. It is hypothesized that hydrophobic catalysis be involved in gene recognition and gene recombination mediated by bacterial RecA (one of the oldest proteins we know of) as well as in sexual recombination in higher organisms, by Rad51. Hydrophobically catalyzed unstacking fluctuations of DNA bases can favor elongated conformations, such as the recently proposed [Formula: see text]-DNA, with potential regulatory roles. That living cells can survive as dormant spores, with very low water content and in principle as such travel far in space is reflected upon: a random walk model with solar photon pressure as driving force indicates our life on earth could not have originated outside our galaxy but possibly from many solar systems within it — at some place, though, where there was plenty of liquid water.

scholarly journals Biomonitoring of Heavy Metal Pollution Using Acanthocephalans Parasite in Ecosystem: An Updated Overview

Animals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 811 ◽  
Author(s):  
El-Sayed E. Mehana ◽  
Asmaa F. Khafaga ◽  
Samar S. Elblehi ◽  
Mohamed E. Abd El-Hack ◽  
Mohammed A.E. Naiel ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Industrial Revolution ◽  
Heavy Metal Contamination ◽  
Developmental Stages ◽  
Heavy Metal Accumulation ◽  
Natural Ecosystem ◽  
Parasitic Infestation ◽  
Living Organisms ◽  
Life On Earth

As a result of the global industrial revolution, contamination of the ecosystem by heavy metals has given rise to one of the most important ecological and organismic problems, particularly human, early developmental stages of fish and animal life. The bioaccumulation of heavy metals in fish tissues can be influenced by several factors, including metal concentration, exposure time, method of metal ingestion and environmental conditions, such as water temperature. Upon recognizing the danger of contamination from heavy metals and the effects on the ecosystem that support life on earth, new ways of monitoring and controlling this pollution, besides the practical ones, had to be found. Diverse living organisms, such as insects, fish, planktons, livestock and bacteria can be used as bioindicators for monitoring the health of the natural ecosystem of the environment. Parasites have attracted intense interest from parasitic ecologists, because of the variety of different ways in which they respond to human activity contamination as prospective indices of environmental quality. Previous studies showed that fish intestinal helminths might consider potential bioindicators for heavy metal contamination in aquatic creatures. In particular, cestodes and acanthocephalans have an increased capacity to accumulate heavy metals, where, for example, metal concentrations in acanthocephalans were several thousand times higher than in host tissues. On the other hand, parasitic infestation in fish could induce significant damage to the physiologic and biochemical processes inside the fish body. It may encourage serious impairment to the physiologic and general health status of fish. Thus, this review aimed to highlight the role of heavy metal accumulation, fish histopathological signs and parasitic infestation in monitoring the ecosystem pollutions and their relationship with each other.

scholarly journals Replaying the tape of life in the twenty-first century

2015 ◽  
Vol 5 (6) ◽  
pp. 20150057 ◽  
Author(s):  
Virginie Orgogozo
Keyword(s):  
Experimental Evolution ◽  
First Century ◽  
Phenotypic Evolution ◽  
Phenotypic Differences ◽  
Diverse Species ◽  
Evolution Of Life ◽  
Long Time ◽  
Time Periods ◽  
Living Organisms ◽  
Life On Earth

Should the tape of life be replayed, would it produce similar living beings? A classical answer has long been ‘no’, but accumulating data are now challenging this view. Repeatability in experimental evolution, in phenotypic evolution of diverse species and in the genes underlying phenotypic evolution indicates that despite unpredictability at the level of basic evolutionary processes (such as apparition of mutations), a certain kind of predictability can emerge at higher levels over long time periods. For instance, a survey of the alleles described in the literature that cause non-deleterious phenotypic differences among animals, plants and yeasts indicates that similar phenotypes have often evolved in distinct taxa through independent mutations in the same genes. Does this mean that the range of possibilities for evolution is limited? Does this mean that we can predict the outcomes of a replayed tape of life? Imagining other possible paths for evolution runs into four important issues: (i) resolving the influence of contingency, (ii) imagining living organisms that are different from the ones we know, (iii) finding the relevant concepts for predicting evolution, and (iv) estimating the probability of occurrence for complex evolutionary events that occurred only once during the evolution of life on earth.

Science and creativity

2020 ◽  
Author(s):  
Flavia Bruno
Keyword(s):  
Chemical Reactions ◽  
Scientific Conference ◽  
Scientific Terminology ◽  
Educational Standard ◽  
The Earth ◽  
Hands On ◽  
Earth Structures ◽  
Lithospheric Plates ◽  
Living Organisms

&lt;p&gt;I teach Natural Sciences in a Liceo Artistico, a type of secondary school in Italy. It is designed to give students the skills to progress to any university, but specifically devoted to art related topics.&lt;br&gt;During my career I have been following the national educational standard of the Ministero dell&amp;#8217;Istruzione, dell&amp;#8217;Universit&amp;#224; e della Ricerca of my Country.&lt;br&gt;During the years students are involved in meaningful hands-on activities &amp;#160; such as the study of the rocks in the country, preparation of easy chemical reactions and observations through a microscope of vegetal and animal organisms. These last ones are very interesting in a Liceo Artistico where many topics focus on the study of the morphology.&lt;br&gt;The theory confirms what the students learn during the practical activities, furthermore it is important to acquire a correct scientific terminology as well as to be able to express scientific issues.&lt;br&gt;I teach during the year the following main topics:&lt;br&gt;Science of Earth: the Solar System, the two motions of the Earth, structures of the Earth surface (rivers, lakes, glaciers, oceans and seas), the Earth&amp;#8217;s Spheres, the movement of lithospheric plates.&lt;br&gt;Biology: the characteristics and functions of living organisms especially the cells and the biodiversity. The Evolution, Mendel&amp;#8217;s genetic laws, organism-environment relationship in order to valorize and to maintain the biodiversity. Chemistry: state of matter, classification of matter, the Mendeleev&amp;#8217;s Periodic Table, the main chemical reactions, atomics models, chemical bonds, chemical nomenclature.&lt;br&gt;The extra-curricular course proposal of my school (POFT-Piano dell&amp;#8217;Offerta Formativa Triennale) includes my project whose title is &amp;#8220;Science and creativity&amp;#8221;. The achievement is to create a link between scientific subjects and the art ones in order to approach knowledge which appear distant but have really many points to share.&lt;br&gt;Every year some classrooms study different topics such as the Nanoparticles, Biomimetic and this year the Adaptations of the animals.&lt;br&gt;After a scientific conference, plastic models and graphic drawings will be realised by the students, who starting from the scientific reality, can express their creativity.&lt;br&gt;During the years I organize some educational visits for example to the Botanic Garden as well as to the countryside; in this way the students have opportunities to create an e-book with texts and photographs.&lt;br&gt;For instance two years ago my classroom created an e-book with botanical cards and the following year another one with the title &amp;#8220;Rocce a Milano&amp;#8221; where students took pictures and texts about this topic.&lt;br&gt;Many classrooms and teachers are involved in this project for example Plastic and Drawing teachers, as well as Multimedia teachers. I manage to gather the interested teachers and to realize the projects.&lt;br&gt;With our productions we participate in competitions and we are sometimes selected.&lt;/p&gt;

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