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Biochemistry (ACS Publications)

Alternative title: physiological chemistry

Biochemistry,study of the chemical substances and processes that occur in plants, animals, and microorganisms and of the changes they undergo during development and life. It deals with the chemistry of life, and as such it draws on the techniques of analytical, organic, and physical chemistry, as well as those of physiologists concerned with the molecular basis of vital processes. All chemical changes within the organismeither the degradation of substances, generally to gain necessary energy, or the buildup of complex molecules necessary for life processesare collectively termed metabolism. These chemical changes depend on the action of organic catalysts known as ... (100 of 5,651 words)

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biochemistry | science | Britannica.com

The key thing to remember is that biochemistry is the chemistry of the living world. Plants, animals, and single-celled organisms all use the same basic chemical compounds to live their lives. Biochemistry is not about the cells or the organisms. It's about the smallest parts of those organisms, the molecules. It's also about the cycles that create those biological compounds.

Every cycle has a place, and each one is just a small piece that helps an organism survive. In each cycle, molecules are used as reactants and then transformed into products. Life is one big network of activity where each piece relies on all of the others. A compound, such as an herbicide, may only break one part of one cycle in a plant. However, because everything needs to work together, the whole plant eventually dies.

We like biochemistry because we learn about things that are inside of us. We can relate to what happens when we eat and how our bodies are constructed. We can imagine how the molecules are moving around the mitochondria or chloroplasts, as opposed to chemical changes that make natural gas. If you choose a career in biology or chemistry, you will need to understand the information in both biochemistry and organic chemistry. Why? Because the movement of atoms in the bio-chem world follows the same rules you will learn in o-chem.

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Chem4Kids.com: Biochemistry

Molecular Visualization Activities

Sorry, the software needed for the activities is no longer available.

Chemistry Review the basics of chemistry you'll need to know to study biology.

Large Molecules Learn about structures and properties of sugars, lipids, amino acids, and nucleotides, as well as macromolecules including proteins, nucleic acids and polysaccharides.

Chemistry of Amino Acids learn the structure and chemistry of the amino acids that are found within proteins.

Acids & Bases Learn about the solvent properties of water, pH, pKa and buffering capacity.

Clinical Correlates of pH Levels Learn how metabolic acidosis or alkalosis can arise and how these conditions shift the bicarbonate equilibrium. The body's compensatory mechanisms and treatment options are also discussed.

B12/Folate Learn which biological reactions require either B12 or folate (or both); what the consequences of a deficiency in either vitamin are, and the important step in which B12 and folate metabolism overlap.

Metabolism Develop a basic understanding of some of the fundamental concepts of metabolism

Carbohydrate Metabolism Regulation Learn about the regulation of carbohydrate metabolism by insulin, glucagon and epinephrine, mainly in liver and muscle.

Photosynthesis 1 Study the conversion of light energy into different forms of chemical energy during photosynthesis.

Photosynthesis 2 Review the location and overall reactions of carbohydrate biosynthesis during photosynthesis, and understand the metabolic differences between C3 and C4 plants

Entrez, provided by the National Center for Biotechnology Information, is a thorough WWW resource worth exploring.

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The Biology Project: Biochemistry

Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms.[1] By controlling information flow through biochemical signaling and the flow of chemical energy through metabolism, biochemical processes give rise to the complexity of life. Over the last decades of the 20th century, biochemistry has become so successful at explaining living processes that now almost all areas of the life sciences from botany to medicine to genetics are engaged in biochemical research.[2] Today, the main focus of pure biochemistry is in understanding how biological molecules give rise to the processes that occur within living cells, which in turn relates greatly to the study and understanding of whole organisms.

Biochemistry is closely related to molecular biology, the study of the molecular mechanisms by which genetic information encoded in DNA is able to result in the processes of life. Depending on the exact definition of the terms used, molecular biology can be thought of as a branch of biochemistry, or biochemistry as a tool with which to investigate and study molecular biology.

Much of biochemistry deals with the structures, functions and interactions of biological macromolecules, such as proteins, nucleic acids, carbohydrates and lipids, which provide the structure of cells and perform many of the functions associated with life. The chemistry of the cell also depends on the reactions of smaller molecules and ions. These can be inorganic, for example water and metal ions, or organic, for example the amino acids which are used to synthesize proteins. The mechanisms by which cells harness energy from their environment via chemical reactions are known as metabolism. The findings of biochemistry are applied primarily in medicine, nutrition, and agriculture. In medicine, biochemists investigate the causes and cures of disease. In nutrition, they study how to maintain health and study the effects of nutritional deficiencies. In agriculture, biochemists investigate soil and fertilizers, and try to discover ways to improve crop cultivation, crop storage and pest control.

At its broadest definition, biochemistry can be seen as a study of the components and composition of living things and how they come together to become life, and the history of biochemistry may therefore go back as far as the ancient Greeks.[3] However, biochemistry as a specific scientific discipline has its beginning some time in the 19th century, or a little earlier, depending on which aspect of biochemistry is being focused on. Some argued that the beginning of biochemistry may have been the discovery of the first enzyme, diastase (today called amylase), in 1833 by Anselme Payen,[4] while others considered Eduard Buchner's first demonstration of a complex biochemical process alcoholic fermentation in cell-free extracts in 1897 to be the birth of biochemistry.[5][6] Some might also point as its beginning to the influential 1842 work by Justus von Liebig, Animal chemistry, or, Organic chemistry in its applications to physiology and pathology, which presented a chemical theory of metabolism,[3] or even earlier to the 18th century studies on fermentation and respiration by Antoine Lavoisier.[7][8] Many other pioneers in the field who helped to uncover the layers of complexity of biochemistry have been proclaimed founders of modern biochemistry, for example Emil Fischer for his work on the chemistry of proteins,[9] and F. Gowland Hopkins on enzymes and the dynamic nature of biochemistry.[10]

The term "biochemistry" itself is derived from a combination of biology and chemistry. In 1877, Felix Hoppe-Seyler used the term (biochemie in German) as a synonym for physiological chemistry in the foreword to the first issue of Zeitschrift fr Physiologische Chemie (Journal of Physiological Chemistry) where he argued for the setting up of institutes dedicated to this field of study.[11][12] The German chemist Carl Neuberg however is often cited to have been coined the word in 1903,[13][14][15] while some credited it to Franz Hofmeister.[16]

It was once generally believed that life and its materials had some essential property or substance (often referred to as the "vital principle") distinct from any found in non-living matter, and it was thought that only living beings could produce the molecules of life.[17] Then, in 1828, Friedrich Whler published a paper on the synthesis of urea, proving that organic compounds can be created artificially.[18] Since then, biochemistry has advanced, especially since the mid-20th century, with the development of new techniques such as chromatography, X-ray diffraction, dual polarisation interferometry, NMR spectroscopy, radioisotopic labeling, electron microscopy, and molecular dynamics simulations. These techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle (citric acid cycle).

Another significant historic event in biochemistry is the discovery of the gene and its role in the transfer of information in the cell. This part of biochemistry is often called molecular biology.[19] In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, and Maurice Wilkins were instrumental in solving DNA structure and suggesting its relationship with genetic transfer of information.[20] In 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme.[21] In 1988, Colin Pitchfork was the first person convicted of murder with DNA evidence, which led to growth of forensic science.[22] More recently, Andrew Z. Fire and Craig C. Mello received the 2006 Nobel Prize for discovering the role of RNA interference (RNAi), in the silencing of gene expression.[23]

Around two dozen of the 92 naturally occurring chemical elements are essential to various kinds of biological life. Most rare elements on Earth are not needed by life (exceptions being selenium and iodine), while a few common ones (aluminum and titanium) are not used. Most organisms share element needs, but there are a few differences between plants and animals. For example, ocean algae use bromine but land plants and animals seem to need none. All animals require sodium, but some plants do not. Plants need boron and silicon, but animals may not (or may need ultra-small amounts).

Just six elementscarbon, hydrogen, nitrogen, oxygen, calcium, and phosphorusmake up almost 99% of the mass of a human body (see composition of the human body for a complete list). In addition to the six major elements that compose most of the human body, humans require smaller amounts of possibly 18 more.[24]

The four main classes of molecules in biochemistry (often called biomolecules) are carbohydrates, lipids, proteins, and nucleic acids. Many biological molecules are polymers: in this terminology, monomers are relatively small micromolecules that are linked together to create large macromolecules known as polymers. When monomers are linked together to synthesize a biological polymer, they undergo a process called dehydration synthesis. Different macromolecules can assemble in larger complexes, often needed for biological activity.

The function of carbohydrates includes energy storage and providing structure. Sugars are carbohydrates, but not all carbohydrates are sugars. There are more carbohydrates on Earth than any other known type of biomolecule; they are used to store energy and genetic information, as well as play important roles in cell to cell interactions and communications.

The simplest type of carbohydrate is a monosaccharide, which between other properties contains carbon, hydrogen, and oxygen, mostly in a ratio of 1:2:1 (generalized formula CnH2nOn, where n is at least 3). Glucose (C6H12O6) is one of the most important carbohydrates, others include fructose (C6H12O6), the sugar commonly associated with the sweet taste of fruits,[25][a] and deoxyribose (C5H10O4).

When two monosaccharides undergo dehydration synthesis whereby a molecule of water is released, as two hydrogen atoms and one oxygen atom are lost from the two monosaccharides. The new molecule, consisting of two monosaccharides, is called a disaccharide and is conjoined together by a glycosidic or ether bond. The reverse reaction can also occur, using a molecule of water to split up a disaccharide and break the glycosidic bond; this is termed hydrolysis. The most well-known disaccharide is sucrose, ordinary sugar (in scientific contexts, called table sugar or cane sugar to differentiate it from other sugars). Sucrose consists of a glucose molecule and a fructose molecule joined together. Another important disaccharide is lactose, consisting of a glucose molecule and a galactose molecule. As most humans age, the production of lactase, the enzyme that hydrolyzes lactose back into glucose and galactose, typically decreases. This results in lactase deficiency, also called lactose intolerance.

When a few (around three to six) monosaccharides are joined, it is called an oligosaccharide (oligo- meaning "few"). These molecules tend to be used as markers and signals, as well as having some other uses. Many monosaccharides joined together make a polysaccharide. They can be joined together in one long linear chain, or they may be branched. Two of the most common polysaccharides are cellulose and glycogen, both consisting of repeating glucose monomers. Examples are Cellulose which is an important structural component of plant's cell walls, and glycogen, used as a form of energy storage in animals.

Sugar can be characterized by having reducing or non-reducing ends. A reducing end of a carbohydrate is a carbon atom that can be in equilibrium with the open-chain aldehyde (aldose) or keto form (ketose). If the joining of monomers takes place at such a carbon atom, the free hydroxy group of the pyranose or furanose form is exchanged with an OH-side-chain of another sugar, yielding a full acetal. This prevents opening of the chain to the aldehyde or keto form and renders the modified residue non-reducing. Lactose contains a reducing end at its glucose moiety, whereas the galactose moiety form a full acetal with the C4-OH group of glucose. Saccharose does not have a reducing end because of full acetal formation between the aldehyde carbon of glucose (C1) and the keto carbon of fructose (C2).

Lipids comprises a diverse range of molecules and to some extent is a catchall for relatively water-insoluble or nonpolar compounds of biological origin, including waxes, fatty acids, fatty-acid derived phospholipids, sphingolipids, glycolipids, and terpenoids (e.g., retinoids and steroids). Some lipids are linear aliphatic molecules, while others have ring structures. Some are aromatic, while others are not. Some are flexible, while others are rigid.[26] are usually made from one molecule of glycerol combined with other molecules. In triglycerides, the main group of bulk lipids, there is one molecule of glycerol and three fatty acids. Fatty acids are considered the monomer in that case, and may be saturated (no double bonds in the carbon chain) or unsaturated (one or more double bonds in the carbon chain).

Most lipids have some polar character in addition to being largely nonpolar. In general, the bulk of their structure is nonpolar or hydrophobic ("water-fearing"), meaning that it does not interact well with polar solvents like water. Another part of their structure is polar or hydrophilic ("water-loving") and will tend to associate with polar solvents like water. This makes them amphiphilic molecules (having both hydrophobic and hydrophilic portions). In the case of cholesterol, the polar group is a mere -OH (hydroxyl or alcohol). In the case of phospholipids, the polar groups are considerably larger and more polar, as described below.

Lipids are an integral part of our daily diet. Most oils and milk products that we use for cooking and eating like butter, cheese, ghee etc., are composed of fats. Vegetable oils are rich in various polyunsaturated fatty acids (PUFA). Lipid-containing foods undergo digestion within the body and are broken into fatty acids and glycerol, which are the final degradation products of fats and lipids. Lipids, especially phospholipids, are also used in various pharmaceutical products, either as co-solubilisers (e.g., in parenteral infusions) or else as drug carrier components (e.g., in a liposome or transfersome).

Proteins are very large molecules macro-biopolymers made from monomers called amino acids. An amino acid consists of a carbon atom bound to four groups. One is an amino group, NH2, and one is a carboxylic acid group, COOH (although these exist as NH3+ and COO under physiologic conditions). The third is a simple hydrogen atom. The fourth is commonly denoted "R" and is different for each amino acid. There are 20 standard amino acids, each containing a carboxyl group, an amino group, and a side-chain (known as an "R" group). The "R" group is what makes each amino acid different, and the properties of the side-chains greatly influence the overall three-dimensional conformation of a protein. Some amino acids have functions by themselves or in a modified form; for instance, glutamate functions as an important neurotransmitter.Amino acids can be joined via a peptide bond. In this dehydration synthesis, a water molecule is removed and the peptide bond connects the nitrogen of one amino acid's amino group to the carbon of the other's carboxylic acid group. The resulting molecule is called a dipeptide, and short stretches of amino acids (usually, fewer than thirty) are called peptides or polypeptides. Longer stretches merit the title proteins. As an example, the important blood serum protein albumin contains 585 amino acid residues.[27]

Some proteins perform largely structural roles. For instance, movements of the proteins actin and myosin ultimately are responsible for the contraction of skeletal muscle. One property many proteins have is that they specifically bind to a certain molecule or class of moleculesthey may be extremely selective in what they bind. Antibodies are an example of proteins that attach to one specific type of molecule. In fact, the enzyme-linked immunosorbent assay (ELISA), which uses antibodies, is one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins, however, are the enzymes. These molecules recognize specific reactant molecules called substrates; they then catalyze the reaction between them. By lowering the activation energy, the enzyme speeds up that reaction by a rate of 1011 or more: a reaction that would normally take over 3,000 years to complete spontaneously might take less than a second with an enzyme. The enzyme itself is not used up in the process, and is free to catalyze the same reaction with a new set of substrates. Using various modifiers, the activity of the enzyme can be regulated, enabling control of the biochemistry of the cell as a whole.

The structure of proteins is traditionally described in a hierarchy of four levels. The primary structure of a protein simply consists of its linear sequence of amino acids; for instance, "alanine-glycine-tryptophan-serine-glutamate-asparagine-glycine-lysine-". Secondary structure is concerned with local morphology (morphology being the study of structure). Some combinations of amino acids will tend to curl up in a coil called an -helix or into a sheet called a -sheet; some -helixes can be seen in the hemoglobin schematic above. Tertiary structure is the entire three-dimensional shape of the protein. This shape is determined by the sequence of amino acids. In fact, a single change can change the entire structure. The alpha chain of hemoglobin contains 146 amino acid residues; substitution of the glutamate residue at position 6 with a valine residue changes the behavior of hemoglobin so much that it results in sickle-cell disease. Finally, quaternary structure is concerned with the structure of a protein with multiple peptide subunits, like hemoglobin with its four subunits. Not all proteins have more than one subunit.[28]

Ingested proteins are usually broken up into single amino acids or dipeptides in the small intestine, and then absorbed. They can then be joined to make new proteins. Intermediate products of glycolysis, the citric acid cycle, and the pentose phosphate pathway can be used to make all twenty amino acids, and most bacteria and plants possess all the necessary enzymes to synthesize them. Humans and other mammals, however, can synthesize only half of them. They cannot synthesize isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. These are the essential amino acids, since it is essential to ingest them. Mammals do possess the enzymes to synthesize alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine, the nonessential amino acids. While they can synthesize arginine and histidine, they cannot produce it in sufficient amounts for young, growing animals, and so these are often considered essential amino acids.

If the amino group is removed from an amino acid, it leaves behind a carbon skeleton called an -keto acid. Enzymes called transaminases can easily transfer the amino group from one amino acid (making it an -keto acid) to another -keto acid (making it an amino acid). This is important in the biosynthesis of amino acids, as for many of the pathways, intermediates from other biochemical pathways are converted to the -keto acid skeleton, and then an amino group is added, often via transamination. The amino acids may then be linked together to make a protein.[29]

A similar process is used to break down proteins. It is first hydrolyzed into its component amino acids. Free ammonia (NH3), existing as the ammonium ion (NH4+) in blood, is toxic to life forms. A suitable method for excreting it must therefore exist. Different tactics have evolved in different animals, depending on the animals' needs. Unicellular organisms, of course, simply release the ammonia into the environment. Likewise, bony fish can release the ammonia into the water where it is quickly diluted. In general, mammals convert the ammonia into urea, via the urea cycle.[30]

In order to determine whether two proteins are related, or in other words to decide whether they are homologous or not, scientists use sequence-comparison methods. Methods like Sequence Alignments and Structural Alignments are powerful tools that help scientists identify homologies between related molecules.[31] The relevance of finding homologies among proteins goes beyond forming an evolutionary pattern of protein families. By finding how similar two protein sequences are, we acquire knowledge about their structure and therefore their function.

Nucleic acids, so called because of its prevalence in cellular nuclei, is the generic name of the family of biopolymers. They are complex, high-molecular-weight biochemical macromolecules that can convey genetic information in all living cells and viruses.[32] The monomers are called nucleotides, and each consists of three components: a nitrogenous heterocyclic base (either a purine or a pyrimidine), a pentose sugar, and a phosphate group. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).[33] The phosphate group and the sugar of each nucleotide bond with each other to form the backbone of the nucleic acid, while the sequence of nitrogenous bases stores the information. The most common nitrogenous bases are adenine, cytosine, guanine, thymine, and uracil. The nitrogenous bases of each strand of a nucleic acid will form hydrogen bonds with certain other nitrogenous bases in a complementary strand of nucleic acid (similar to a zipper). Adenine binds with thymine and uracil; Thymine binds only with adenine; and cytosine and guanine can bind only with one another.

Aside from the genetic material of the cell, nucleic acids often play a role as second messengers, as well as forming the base molecule for adenosine triphosphate (ATP), the primary energy-carrier molecule found in all living organisms. Also, the nitrogenous bases possible in the two nucleic acids are different: adenine, cytosine, and guanine occur in both RNA and DNA, while thymine occurs only in DNA and uracil occurs in RNA.

Glucose is the major energy source in most life forms. For instance, polysaccharides are broken down into their monomers (glycogen phosphorylase removes glucose residues from glycogen). Disaccharides like lactose or sucrose are cleaved into their two component monosaccharides.

Glucose is mainly metabolized by a very important ten-step pathway called glycolysis, the net result of which is to break down one molecule of glucose into two molecules of pyruvate; this also produces a net two molecules of ATP, the energy currency of cells, along with two reducing equivalents as converting NAD+ to NADH. This does not require oxygen; if no oxygen is available (or the cell cannot use oxygen), the NAD is restored by converting the pyruvate to lactate (lactic acid) (e.g., in humans) or to ethanol plus carbon dioxide (e.g., in yeast). Other monosaccharides like galactose and fructose can be converted into intermediates of the glycolytic pathway.[34]

In aerobic cells with sufficient oxygen, as in most human cells, the pyruvate is further metabolized. It is irreversibly converted to acetyl-CoA, giving off one carbon atom as the waste product carbon dioxide, generating another reducing equivalent as NADH. The two molecules acetyl-CoA (from one molecule of glucose) then enter the citric acid cycle, producing two more molecules of ATP, six more NADH molecules and two reduced (ubi)quinones (via FADH2 as enzyme-bound cofactor), and releasing the remaining carbon atoms as carbon dioxide. The produced NADH and quinol molecules then feed into the enzyme complexes of the respiratory chain, an electron transport system transferring the electrons ultimately to oxygen and conserving the released energy in the form of a proton gradient over a membrane (inner mitochondrial membrane in eukaryotes). Thus, oxygen is reduced to water and the original electron acceptors NAD+ and quinone are regenerated. This is why humans breathe in oxygen and breathe out carbon dioxide. The energy released from transferring the electrons from high-energy states in NADH and quinol is conserved first as proton gradient and converted to ATP via ATP synthase. This generates an additional 28 molecules of ATP (24 from the 8 NADH + 4 from the 2 quinols), totaling to 32 molecules of ATP conserved per degraded glucose (two from glycolysis + two from the citrate cycle). It is clear that using oxygen to completely oxidize glucose provides an organism with far more energy than any oxygen-independent metabolic feature, and this is thought to be the reason why complex life appeared only after Earth's atmosphere accumulated large amounts of oxygen.

In vertebrates, vigorously contracting skeletal muscles (during weightlifting or sprinting, for example) do not receive enough oxygen to meet the energy demand, and so they shift to anaerobic metabolism, converting glucose to lactate. The liver regenerates the glucose, using a process called gluconeogenesis. This process is not quite the opposite of glycolysis, and actually requires three times the amount of energy gained from glycolysis (six molecules of ATP are used, compared to the two gained in glycolysis). Analogous to the above reactions, the glucose produced can then undergo glycolysis in tissues that need energy, be stored as glycogen (or starch in plants), or be converted to other monosaccharides or joined into di- or oligosaccharides. The combined pathways of glycolysis during exercise, lactate's crossing via the bloodstream to the liver, subsequent gluconeogenesis and release of glucose into the bloodstream is called the Cori cycle.[35]

Researchers in biochemistry use specific techniques native to biochemistry, but increasingly combine these with techniques and ideas developed in the fields of genetics, molecular biology and biophysics. There has never been a hard-line among these disciplines in terms of content and technique. Today, the terms molecular biology and biochemistry are nearly interchangeable. The following figure is a schematic that depicts one possible view of the relationship between the fields:

a. ^ Fructose is not the only sugar found in fruits. Glucose and sucrose are also found in varying quantities in various fruits, and indeed sometimes exceed the fructose present. For example, 32% of the edible portion of date is glucose, compared with 23.70% fructose and 8.20% sucrose. However, peaches contain more sucrose (6.66%) than they do fructose (0.93%) or glucose (1.47%).[37]

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Biochemistry - Wikipedia, the free encyclopedia

Review

Part I: MOLECULAR COMPONENTS OF CELLS. 1. Chemistry is the Logic of Biological Phenomena. 2. Water-The Medium of Life. 3. Thermodynamics of Biological Systems. 4. Amino Acids. 5. Proteins: Their Primary Structure and Biological Functions. 6. Proteins: Secondary, Tertiary, and Quaternary Structure. 7. Carbohydrates and Glyco-Conjugates of the Cell Surface. 8. Lipids. 9. Membranes and Membrane Transport. 10. Nucleotides and Nucleic Acids. 11. Structure of Nucleic Acids. 12. Recombinant DNA: Cloning and Creation of Chimeric Genes. Part II: PROTEIN DYNAMICS. 13. Enzyme Kinetics. 14. Mechanisms of Enzyme Action. 15. Enzyme Regulation. 16. Molecular Motors. Part III: METABOLISM AND ITS REGULATION. 17. Nutrition and the Organization of Metabolism. 18. Glycolysis. 19. The Tricarboxylic Acid Cycle. 20. Electron Transport and Oxidative Phosphorylation. 21. Photosynthesis. 22. Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway. 23. Fatty Acid Catabolism. 24. Lipid Biosynthesis. 25. Nitrogen Acquisition and Amino Acid Metabolism. 26. The Synthesis and Degradation of Nucleotides. 27. Metabolic Integration and Organ Specialization. Part IV: INFORMATION TRANSFER. 28. DNA Metabolism. 29. Transcription and the Regulation of Gene Expression. 30. Protein Synthesis. 31. Post-Translational Processing of Proteins and Protein Degradation. 32. The Reception and Transmission of Extracellular Information. --This text refers to the Paperback edition.

Reginald H. Garrett was educated in the Baltimore city public schools and at the Johns Hopkins University, where he received his Ph.D. in biology in 1968. Since that time, he has conducted research and taught biochemistry courses at the University of Virginia, where he is currently Professor of Biology. He is the author of numerous papers and review articles on biochemical, genetic, and molecular biological aspects of inorganic nitrogen metabolism. His early research focused on the pathway of nitrate assimilation in filamentous fungi. His investigations contributed substantially to our understanding of the enzymology, genetics, and regulation of this major pathway of biological nitrogen acquisition. More recently, he has collaborated in systems approaches to the metabolic basis of nutrition-related diseases. His research has been supported by grants from the National Institutes of Health, the National Science Foundation, and private industry. A member of the American Society for Biochemistry and Molecular Biology, Garrett is a former Fulbright Scholar, was twice Visiting Scholar at the University of Cambridge, and was Invited Professor at the University of Toulouse, France.

Charles M. Grisham received his B.S. in chemistry from the Illinois Institute of Technology in 1969 and his Ph.D. in chemistry from the University of Minnesota in 1973. Following a postdoctoral appointment at the Institute for Cancer Research in Philadelphia, he became Professor of Chemistry at the University of Virginia, where he teaches biochemistry, introductory chemistry, and physical chemistry. He has authored numerous papers and review articles on active transport of sodium, potassium, and calcium in mammalian systems, on protein kinase C, and on the applications of NMR and EPR spectroscopy to the study of biological systems. His work has been supported by the National Institutes of Health, the National Science Foundation, the Muscular Dystrophy Association of America, the Research Corporation, the American Heart Association and the American Chemical Society. A member of the American Society for Biochemistry and Molecular Biology, Grisham held the Knapp Chair in Chemistry in 1999 at the University of San Diego; was Visiting Scientist at the Aarhus University Institute of Physiology, Aarhus, Denmark, for two years; and received a Research Career Development Award from the National Institutes of Health.

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Amazon.com: Biochemistry (9781133106296): Reginald H ...

Biology Week 2015-an annual celebration of the biosciences

This year's events include science festivals, Big Biology Days,dino digs,competitions,lectures, andmusic and storytelling. The events are running from Saturday 10th - Sunday 18th October. You can start the week by taking theBiology Week Quizand finally finding out whether zebras are black with white stripes or white with black stripes.

Tomas Lindahl,Paul ModrichandAziz Sancarhave been jointly awarded the2015 Nobel Prize in Chemistryfor their work on mechanistic studies of DNA repair.

Do you know of an outstanding bioscientist that deserves recognition? Nominations can be submitted by both members and non-members of the Biochemical Society.

Deadline for online nominations is 31 January 2016

The Impact Factors and journal metrics for the range of molecular bioscience journals published by Portland Press, the knowledge hub for life sciences, have been announced. The 2015 Release of Journal Citation Reports (Source: 2014 Web of ScienceTM Data) shows an increase in article influence scores indicating that the research being published and cited in Portland Press journals carries influence scores above the average in its field.

The announcement of these metrics comes in the middle of an exciting year for Portland Press. Having just migrated all its journals to new websites offering a range of new features and improved discoverability for authors work, further developments are planned for the remainder of 2015.

The Biochemical Society wants to reaffirm its commitment to the promotion of equality and diversity in the life science sector. It is especially concerned about the promotion of careers for women in science, but also believes in full integration and opportunities, irrespective of a person's race, class, sexuality, beliefs or innate ability. The Society believes that science, and indeed all human efforts, benefit from diverse inputs, and that everyone loses by disfavouring specific groups. Hence, the Society dissociates itself from the reported recent comments of Sir Tim Hunt, during his visit to South Korea. The Society recognises and espouses the right to free speech and the expression of diverse points of view, but this right comes with the proviso of responsible use, and the ensuing right to free debate.

New look for Portland Press journals

Portland Press, the wholly-owned trading subsidiary of the Biochemical Society has launched its journals on a new website.

The new websites have been designed to adapt to the latest advances in online publishing and will offer improved services to authors, readers and subscribers, including Biochemical Society members. Authors will enjoy greater visibility for their articles and readers will see an improved experience when searching for work published in the journals.

The journals enjoying a new look are:

Clinical Science Biochemical Journal Bioscience Reports Biochemical Society Transactions Essays in Biochemistry

Biochemical Society members enjoy free full-text access to Biochemical Journal and Biochemical Society Transactions - members should visit theMembers' Areato access

As part of its commitment to advance biochemistry for the benefit of science and society, the Biochemical Society makes available via its publisher Portland Press, two resources,Cell Signalling Biologyand Glossary of Biochemistry and Molecular Biology entirely free of charge to the community and both of these also have a new look as part of the move.

If you have any questions or feedback for us please do get in touch ateditorial@portlandpress.com

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Biochemical Society | Advancing Molecular Bioscience

Thank you for visiting the Department of Chemistry and Biochemistry. Ours is a vibrant and dynamic Department that combines research on the most consequential and revelatory scientific areas with education aimed at building our future leaders and informed citizens.

The research we engage in is marked by its breadth from atomic to cellular, from origins of life to climate change, from single molecules to systems level, from sustainable energy to cancer cures, from nanomaterials to solar systems, from infectious diseases to semiconductors, from RNA splicing to condensed phases, from protein structure to three-body problems, from lipid maps to stable carbenes, and so on. Along with these areas, we also engage in understanding how best to communicate scientific knowledge to our students. All these research efforts are made possible by the approximately $33M of sponsored research funds raised yearly by our faculty, and the array of advanced technologies acquired by our faculty to probe ever deeper into fundamental questions. Our faculty has been acknowledged for their creativity. We have Nobel Prize winners, members of the National Academy of Sciences, and HHMI Investigators among others.

Research is but one facet of our efforts. The other central facet is teaching. In this, we seek not only to convey the wisdom of ages but also the excitement of new scientific findings. The changes in our daily lives that these discoveries are making are enormous, and the pace at which these discoveries are being made is ever increasing. This means that one of our fundamental tasks is to help students understand what lies at the forefront of knowledge, so that they can understand how best to address current and future problems. We find the daily engagement with students to be energizing, and view scientific breakthroughs to be on equal footing with those moments in which we are able to convey an idea so that a student gets it. We teach 22,000 undergraduates and 2,000 graduate students in our courses. We have 1,000 undergraduate majors along with 40 Masters and 200 PhD students, and we train more than 100 Postdoctoral Researchers.

The Department recognizes that science is carried out in a societal context, and values diversity, equity, and inclusion among its faculty, researchers, and students. Indeed, our faculty is one of the most diverse among Chemistry departments. However, we recognize much work remains to be done and we continue to work towards increasing diversity throughout the Department.

I hope you will take some time to look around and learn about the superb research and teaching going on in the Department of Chemistry and Biochemistry.

Partho Ghosh, Chair

Macromolecular, cryoelectron microscopy and three-dimensional, image-reconstruction techniques.

Chemical Education: Development of context-rich curriculum; Use of collaborative learning strategies in large lectures; Communication of chemistry

Natural product synthesis/biosynthesis, Biological chemistry and enzymology, Metabolic engineering.

Chemical Education: Visual Literacy in Science, Biochemistry Education, Nano Science Education, K-20 Professional Development, and STEM Career Development

Bioinorganic and coordination chemistry. Metalloprotein inhibitors and supramolecular materials.

Dissociation dynamics of transient species, three-body reaction dynamics, novel mass-spectrometric methods

Materials chemistry, surface kinetics of metals/semiconductors, CVD, photo-induced deposition, thin-film spectroscopy.

Biochemistry: phospholipase A2, signal transduction in macrophages, lipid maps, prostaglandin regulation, mass spec of lipids and proteins.

Biomimetic Chemistry, Molecular Imaging, Electrochemistry

Protein Tyrosine Phosphatase, Dual=specific Phosphatase, PTEN

Inorganic and Organometallic Chemistry: Synthesis, Small Molecule Activation and New Transformations.

Electron Transport in Condensed Phases. Dissipation and Relaxation Processes. Non-equilibrium Open Quantum Systems. Molecular Electronics.

Biochemistry and biophysics: transcription, signaling, pre-mRNA splicing, mRNA transport, protein-protein, protein-DNA and protein-RNA interactions

Mechanisms of bacterial and protozoan pathogenesis, and host response against infectious microbes.

Bioorganic chemistry, Supramolecular Chemistry, Bionanotechnology, Materials, Synthesis

Nanotechnologies for analysis of glycan function during development. Glycomaterials for stem cell-based tissue regeneration.

Biophysical chemistry: protein structure, dynamics and folding; 2, 3 and 4D NMR spectroscopy; PCR; equilibrium and kinetic-fluorescence, absorbance and circular dichroism spectroscopies

Biophysical chemistry: Spectroscopic studies of membrane protein folding and dynamics

Structure, function, dynamics and thermodynamics of protein-protein interactions: NMR, mass spectrometry and kinetics

Inorganic, materials, and physical chemistry: electron transfer, catalysis, fixation and utilization of carbon dioxide.

STM/STS of gate oxides on compound semiconductors and adsorbates on organic semiconductor

Theoretical chemical physics: non-equilibrium statistical mechanics; stochastic processes; nonlinear phenomena; complex systems; condensed matter.

Statistical mechanics and computational chemistry, with applications to biological systems

Physical Chemistry: Gas Phase Chemical Kinetics and Photochemistry; Chemistry of Atmospheric Aerosols; Air Pollution in Megacities of the Developing World

Organic chemistry of marine natural products, synthesis, NMR, and biomedical applications

Evolution of catalytic RNAs, and the Origin of Life

Organotransition metal; organic; physical organic; bioorganometallic; synthetic; and inorganic chemistry

NMR structural studies of proteins in membranes and other supramolecular assemblies

Theoretical chemical physics of complex interfaces of relevance to the environment

Physical-organic chemistry: stereoelectronic effects; hydrogen bonding; isotope effects; ionic solvation; naked anions; malonic anhydrides

The application of analytical chemistry to forensic, environmental and industrial chemistry, then bridge these experiences into the classroom. This also includes the role technology and instrumentation play in discovery and problem solving.

Environmental, physical/analytical chemistry: gas/particle processes of tropospheric significance; mass spectrometry; laser-based analysis techniques.

Inorganic chemistry: Small-molecule crystallography, synthesis of transition metal/p-block clusters

Nanomaterials: porous silicon, chemical and biological sensors, biomaterials, electrochemistry

Chemical education: development of computer-based multimedia to assist student learning of complex scientific processes and concepts

Experimental physical chemistry: photochemistry; laser spectroscopy; reaction dynamics of vibrationally excited molecules

Physical chemistry; Optical and magnetic spectroscopy; Fundamental studies of charge transport and solvation; Applications to energy conversion and energy storage.

Structure, Function, Dynamics, and Localization of PKA as a Prototype for the Protein Kinase Superfamily.

Bioinorganic and biophysical chemistry; Metalloprotein structure, function and biosynthesis; Biomaterials

Synthetic, Medicinal, Bioorganic and Biological Chemistry, Methods and Strategies in Natural Products Chemistry

Atmospheric chemistry: physical chemistry of isotope effects; solar system formation

Structure and Function of Introns and Retroelements

Ligand-nucleic acid interactions; Antiviral and antibacterial agents; Fluorescent nucleosides and nucleotides; Cellular delivery vehicles

Chemical biology; design, synthesis, and application of molecular probes of biological function

epigenomics, cellular reprogramming, protein recognition, computational biology, systems biology

Physical chemistry: calculations of the dynamics of complex systems; theoretical geochemistry

Spatio-temporal signaling control of biological self-organization. Signaling networks in innate immunity. Microscopy; Mathematical modeling; Computational image analysis; Systems Biology.

Investigation of charge transfer mechanism in nanomaterials with novel ultrafast spectroscopies

Bioorganic Chemistry, Molecular Self-Assembly, Molecular Synthesis, Materials Chemistry, Bionanotechnology

Theory at the interface of chemistry, condensed matter, and materials physics

Gene Expression Control During Stress; mRNA Localization to Membrane-Less Compartments

Dr. Charles W. Machan

Originally posted here:

UCSD Chemistry and Biochemistry

Hou, TY, Barhoumi, R, Fan, YY, Rivera, GM, Hannoush, RN, McMurray, DN et al.. n-3 polyunsaturated fatty acids suppress CD4(+) T cell proliferation by altering phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2] organization. Biochim. Biophys. Acta. 2015; :. doi: 10.1016/j.bbamem.2015.10.009. PubMed PMID:26476105. .

Hong, W, Wang, Y, Chang, Z, Yang, Y, Pu, J, Sun, T et al.. The identification of novel Mycobacterium tuberculosis DHFR inhibitors and the investigation of their binding preferences by using molecular modelling. Sci Rep. 2015;5 :15328. doi: 10.1038/srep15328. PubMed PMID:26471125. .

Yi, G, Wen, Y, Shu, C, Han, Q, Konan, KV, Li, P et al.. The Hepatitis C Virus NS4B Can Suppress STING Accumulation to Evade Innate Immune Responses. J. Virol. 2015; :. doi: 10.1128/JVI.01720-15. PubMed PMID:26468527. .

Original post:

Department of Biochemistry and Biophysics

Hypothetical types of biochemistry are forms of biochemistry speculated to be scientifically viable but not proven to exist at this time.[2] The kinds of living beings currently known on Earth all use carbon compounds for basic structural and metabolic functions, water as a solvent and DNA or RNA to define and control their form. If life exists on other planets or moons, it may be chemically similar; it is also possible that there are organisms with quite different chemistries[3]for instance involving other classes of carbon compounds, compounds of another element, or another solvent in place of water.

The possibility of life-forms being based on "alternative" biochemistries is the topic of an ongoing scientific discussion, informed by what is known about extraterrestrial environments and about the chemical behaviour of various elements and compounds. It is also a common subject in science fiction.

The element silicon has been much discussed as a hypothetical alternative to carbon. Silicon is in the same group as carbon in the periodic table, and like carbon is tetravalent, although the silicon analogs of organic compounds are generally less stable. Hypothetical alternatives to water include ammonia, which, like water, is a polar molecule, and cosmically abundant; and non-polar hydrocarbon solvents such as methane and ethane, which are known to exist in liquid form on the surface of Titan.

Apart from the prospect of finding different forms of life on other planets or moons, Earth itself has been suggested as a place where a shadow biosphere of biochemically unfamiliar micro-organisms might have lived in the past, or may still exist today.[4][5]

Perhaps the least unusual alternative biochemistry would be one with differing chirality of its biomolecules. In known Earth-based life, amino acids are almost universally of the L form and sugars are of the D form. Molecules of opposite chirality have identical chemical properties to their mirrored forms, so life that used D amino acids or L sugars may be possible; molecules of such a chirality, however, would be incompatible with organisms using the opposing chirality molecules. Amino acids whose chirality is opposite to the norm are found on Earth, and these substances are generally thought to result from decay of organisms of normal chirality. However, physicist Paul Davies speculates that some of them might be products of "anti-chiral" life.[6]

It is questionable, however, whether such a biochemistry would be truly alien. Although it would certainly be an alternative stereochemistry, molecules that are overwhelmingly found in one enantiomer throughout the vast majority of organisms can nonetheless often be found in another enantiomer in different (often basal) organisms such as in comparisons between members of Archea and other domains,[citation needed] making it an open topic whether an alternative stereochemistry is truly novel.

On Earth, all known living things have a carbon-based structure and system. Scientists have speculated about the pros and cons of using atoms other than carbon to form the molecular structures necessary for life, but no one has proposed a theory employing such atoms to form all the necessary structures. However, as Carl Sagan argued, it is very difficult to be certain whether a statement that applies to all life on Earth will turn out to apply to all life throughout the universe.[7] Sagan used the term "carbon chauvinism" for such an assumption.[8] Carl Sagan regarded silicon and germanium as conceivable alternatives to carbon;[8] but, on the other hand, he noted that carbon does seem more chemically versatile and is more abundant in the cosmos.[9]

The silicon atom has been much discussed as the basis for an alternative biochemical system, because silicon has many chemical properties similar to those of carbon and is in the same group of the periodic table, the carbon group. Like carbon, silicon can create molecules that are sufficiently large to carry biological information.[10]

However, silicon has several drawbacks as an alternative to carbon. Silicon, unlike carbon, lacks the ability to form chemical bonds with diverse types of atoms as is necessary for the chemical versatility required for metabolism. Elements creating organic functional groups with carbon include hydrogen, oxygen, nitrogen, phosphorus, sulfur, and metals such as iron, magnesium, and zinc. Silicon, on the other hand, interacts with very few other types of atoms.[10] Moreover, where it does interact with other atoms, silicon creates molecules that have been described as "monotonous compared with the combinatorial universe of organic macromolecules".[10] This is because silicon atoms are much bigger, having a larger mass and atomic radius, and so have difficulty forming double bonds (the double bonded carbon is part of the carbonyl group, a fundamental motif of bio-organic chemistry).

Silanes, which are chemical compounds of hydrogen and silicon that are analogous to the alkane hydrocarbons, are highly reactive with water, and long-chain silanes spontaneously decompose. Molecules incorporating polymers of alternating silicon and oxygen atoms instead of direct bonds between silicon, known collectively as silicones, are much more stable. It has been suggested that silicone-based chemicals would be more stable than equivalent hydrocarbons in a sulfuric-acid-rich environment, as is found in some extraterrestrial locations.[11]

Of the varieties of molecules identified in the interstellar medium as of 1998[update], 84 are based on carbon while only 8 are based on silicon.[12] Moreover, of those 8 compounds, four also include carbon within them. The cosmic abundance of carbon to silicon is roughly 10 to 1. This may suggest a greater variety of complex carbon compounds throughout the cosmos, providing less of a foundation upon which to build silicon-based biologies, at least under the conditions prevalent on the surface of planets. Also, even though Earth and other terrestrial planets are exceptionally silicon-rich and carbon-poor (the relative abundance of silicon to carbon in the Earth's crust is roughly 925:1), terrestrial life is carbon-based. The fact that carbon is used instead of silicon, may be evidence that silicon is poorly suited for biochemistry on Earth-like planets. For example: silicon is less versatile than carbon in forming compounds; the compounds formed by silicon are unstable and it blocks the flow of heat.[13]

Even so, biogenic silica is used by some Earth life, such as the silicate skeletal structure of diatoms. According to the clay hypothesis of A. G. Cairns-Smith, silicate minerals in water played a crucial role in abiogenesis: they replicated their crystal structures, interacted with carbon compounds, and were the precursors of carbon-based life.[14][15]

Silicon compounds may possibly be biologically useful under temperatures or pressures different from the surface of a terrestrial planet, either in conjunction with or in a role less directly analogous to carbon. Polysilanols, the silicon compounds corresponding to sugars, are soluble in liquid nitrogen, suggesting that they could play in role in very low temperature biochemistry.[16][17]

In cinematic and literary science fiction, at a moment when man-made machines cross from nonliving to living, it is often posited, this new form would be the first example of non-carbon-based life. Since the advent of the microprocessor in the late 1960s, these machines are often classed as computers (or computer-guided robots) and filed under "silicon-based life", even though the silicon backing matrix of these processors is not nearly as fundamental to their operation as carbon is for "wet life".

Arsenic, which is chemically similar to phosphorus, while poisonous for most life forms on Earth, is incorporated into the biochemistry of some organisms.[20] Some marine algae incorporate arsenic into complex organic molecules such as arsenosugars and arsenobetaines. Fungi and bacteria can produce volatile methylated arsenic compounds. Arsenate reduction and arsenite oxidation have been observed in microbes (Chrysiogenes arsenatis).[21] Additionally, some prokaryotes can use arsenate as a terminal electron acceptor during anaerobic growth and some can utilize arsenite as an electron donor to generate energy.

It has been speculated that the earliest life forms on Earth may have used arsenic in place of phosphorus in the structure of their DNA.[22] A common objection to this scenario is that arsenate esters are so much less stable to hydrolysis than corresponding phosphate esters that arsenic would not be suitable for this function.[23]

The authors of a 2010 geomicrobiology study, supported in part by NASA, have postulated that a bacterium, named GFAJ-1, collected in the sediments of Mono Lake in eastern California, can employ such 'arsenic DNA' when cultured without phosphorus.[24][25] They proposed that the bacterium may employ high levels of poly--hydroxybutyrate or other means to reduce the effective concentration of water and stabilize its arsenate esters.[25] This claim was heavily criticized almost immediately after publication for the perceived lack of appropriate controls.[26][27] Science writer Carl Zimmer contacted several scientists for an assessment: "I reached out to a dozen experts ... Almost unanimously, they think the NASA scientists have failed to make their case".[28] Other authors were unable to reproduce their results and showed that the NASA scientists had issues with phosphate contamination (3 M), which could sustain extremophile lifeforms.[29]

In addition to carbon compounds, all currently known terrestrial life also requires water as a solvent. This has led to discussions about whether water is the only liquid capable of filling that role. The idea that an extraterrestrial life-form might be based on a solvent other than water has been taken seriously in recent scientific literature by the biochemist Steven Benner,[30] and by the astrobiological committee chaired by John A. Baross.[31] Solvents discussed by the Baross committee include ammonia,[32]sulfuric acid,[33]formamide,[34] hydrocarbons,[34] and (at temperatures much lower than Earth's) liquid nitrogen, or hydrogen in the form of a supercritical fluid.[35]

Carl Sagan once described himself as both a carbon chauvinist and a water chauvinist;[36] however on another occasion he said he was a carbon chauvinist but "not that much of a water chauvinist".[37] He speculated on hydrocarbons,[37]hydrofluoric acid,[38] and ammonia[37][38] as possible alternatives to water.

Some of the properties of water that are important for life processes include a large temperature range over which it is liquid, a high heat capacity (useful for temperature regulation), a large heat of vaporization, and the ability to dissolve a wide variety of compounds. Water is also amphoteric, meaning it can donate and accept an H+ ion, allowing it to act as an acid or a base. This property is crucial in many organic and biochemical reactions, where water serves as a solvent, a reactant, or a product. There are other chemicals with similar properties that have sometimes been proposed as alternatives. Additionally, water has the unusual property of being less dense as a solid (ice) than as a liquid. This is why bodies of water freeze over but do not freeze solid (from the bottom up). If ice were denser than liquid water (as is true for nearly all other compounds), then large bodies of liquid would slowly freeze solid, which would not be conducive to the formation of life. Water as a compound is cosmically abundant, although much of it is in the form of vapour or ice. Subsurface liquid water is considered likely or possible on several of the outer moons: Enceladus (where geysers have been observed), Europa, Titan and Ganymede. Earth is the only world currently known to have stable bodies of liquid water on its surface.

Not all properties of water are necessarily advantageous for life, however.[39] For instance, water ice has a high albedo,[39] meaning that it reflects a significant quantity of light and heat from the Sun. During ice ages, as reflective ice builds up over the surface of the water, the effects of global cooling are increased.[39]

There are some properties that make certain compounds and elements much more favorable than others as solvents in a successful biosphere. The solvent must be able to exist in liquid equilibrium over a range of temperatures the planetary object would normally encounter. Because boiling points vary with the pressure, the question tends not to be does the prospective solvent remain liquid, but at what pressure. For example, hydrogen cyanide has a narrow liquid phase temperature range at 1 atmosphere, but in an atmosphere with the pressure of Venus, with 92 bars (9.2MPa) of pressure, it can indeed exist in liquid form over a wide temperature range.

The ammonia molecule (NH3), like the water molecule, is abundant in the universe, being a compound of hydrogen (the simplest and most common element) with another very common element, nitrogen.[40] The possible role of liquid ammonia as an alternative solvent for life is an idea that goes back at least to 1954, when J.B.S. Haldane raised the topic at a symposium about life's origin.[41]

Numerous chemical reactions are possible in an ammonia solution, and liquid ammonia has chemical similarities with water.[40][42] Ammonia can dissolve most organic molecules at least as well as water does and, in addition, it is capable of dissolving many elemental metals. Haldane made the point that various common water-related organic compounds have ammonia-related analogs; for instance the ammonia-related amine group (-NH2) is analogous to the water-related alcohol group (-OH).[42]

Ammonia, like water, can either accept or donate an H+ ion. When ammonia accepts an H+, it forms the ammonium cation (NH4+), analogous to hydronium (H3O+). When it donates an H+ ion, it forms the amide anion (NH2), analogous to the hydroxide anion (OH).[32] Compared to water, however, ammonia is more inclined to accept an H+ ion, and less inclined to donate one; it is a stronger nucleophile.[32] Ammonia added to water functions as Arrhenius base: it increases the concentration of the anion hydroxide. Conversely, using a solvent system definition of acidity and basicity, water added to liquid ammonia functions as an acid, because it increases the concentration of the cation ammonium.[42] The carbonyl group (C=O), which is much used in terrestrial biochemistry, would not be stable in ammonia solution, but the analogous imine group (C=NH) could be used instead.[32]

However, ammonia has some problems as a basis for life. The hydrogen bonds between ammonia molecules are weaker than those in water, causing ammonia's heat of vaporization to be half that of water, its surface tension to be a third, and reducing its ability to concentrate non-polar molecules through a hydrophobic effect. Gerald Feinberg and Robert Shapiro have questioned whether ammonia could hold prebiotic molecules together well enough to allow the emergence of a self-reproducing system.[43] Ammonia is also flammable in oxygen, and could not exist sustainably in an environment suitable for aerobic metabolism.[44]

A biosphere based on ammonia would likely exist at temperatures or air pressures that are extremely unusual in relation to life on Earth. Life on Earth usually exists within the melting point and boiling point of water at normal pressure, between 0C (273K) and 100C (373K); at normal pressure ammonia's melting and boiling points are between 78C (195K) and 33C (240K). Chemical reactions generally proceed more slowly at a lower temperature. Therefore, ammonia-based life, if it exists, might metabolize more slowly and evolve more slowly than life on Earth.[44] On the other hand, lower temperatures could also enable living systems to use chemical species which at Earth temperatures would be too unstable to be useful.[40]

Ammonia could be a liquid at Earth-like temperatures, but at much higher pressures; for example, at 60 atm, ammonia melts at 77C (196K) and boils at 98C (371K).[32]

Ammonia and ammoniawater mixtures remain liquid at temperatures far below the freezing point of pure water, so such biochemistries might be well suited to planets and moons orbiting outside the water-based habitability zone. Such conditions could exist, for example, under the surface of Saturn's largest moon Titan.[45]

Methane (CH4) is a simple hydrocarbon: that is, a compound of two of the most common elements in the cosmos, hydrogen and carbon. It has a cosmic abundance comparable with ammonia.[40] Hydrocarbons could act as a solvent over a wide range of temperatures, but would lack polarity. Isaac Asimov, the biochemist and science fiction writer, suggested in 1981 that poly-lipids could form a substitute for proteins in a non-polar solvent such as methane.[40] Lakes composed of a mixture of hydrocarbons, including methane and ethane, have been detected on the surface of Titan by the Cassini spacecraft.

There is debate about the effectiveness of methane and other hydrocarbons as a solvent for life compared to water or ammonia.[46][47][48] Water is a stronger solvent than the hydrocarbons, enabling easier transport of substances in a cell.[49] However, water is also more chemically reactive, and can break down large organic molecules through hydrolysis.[46] A life-form whose solvent was a hydrocarbon would not face the threat of its biomolecules being destroyed in this way.[46] Also, the water molecule's tendency to form strong hydrogen bonds can interfere with internal hydrogen bonding in complex organic molecules.[39] Life with a hydrocarbon solvent could make more use of hydrogen bonds within its biomolecules.[46] Moreover, the strength of hydrogen bonds within biomolecules would be appropriate to a low-temperature biochemistry.[46]

Astrobiologist Chris McKay has argued, on thermodynamic grounds, that if life does exist on Titan's surface, using hydrocarbons as a solvent, it is likely also to use the more complex hydrocarbons as an energy source by reacting them with hydrogen, reducing ethane and acetylene to methane.[50] Possible evidence for this form of life on Titan was identified in 2010 by Darrell Strobel of Johns Hopkins University; a greater abundance of molecular hydrogen in the upper atmospheric layers of Titan compared to the lower layers, arguing for a downward diffusion at a rate of roughly 1025 molecules per second and disappearance of hydrogen near Titan's surface. As Strobel noted, his findings were in line with the effects Chris McKay had predicted if methanogenic life-forms were present.[49][50][51] The same year, another study showed low levels of acetylene on Titan's surface, which were interpreted by Chris McKay as consistent with the hypothesis of organisms reducing acetylene to methane.[49] While restating the biological hypothesis, McKay cautioned that other explanations for the hydrogen and acetylene findings are to be considered more likely: the possibilities of yet unidentified physical or chemical processes (e.g. a non-living surface catalyst enabling acetylene to react with hydrogen), or flaws in the current models of material flow.[52] He noted that even a non-biological catalyst effective at 95 K would in itself be a startling discovery.[52]

A hypothetical cell membrane capable of functioning in liquid methane in Titan conditions was computer-modeled in February 2015. Composed of small molecules that contain carbon, hydrogen, and nitrogen, it would have the same stability and flexibility as cell membranes on Earth, which are composed of phospholipids, compounds of carbon, hydrogen, oxygen, and phosphorus. This hypothetical cell membrane was termed an "azotosome", a classical compound made of "azote", French for nitrogen, and "soma", Greek for body, by analogy with "liposome".[53]

Hydrogen fluoride (HF), like water, is a polar molecule, and due to its polarity it can dissolve many ionic compounds. Its melting point is 84C and its boiling point is 19.54C (at atmospheric pressure); the difference between the two is a little more than 100 K. HF also makes hydrogen bonds with its neighbor molecules, as do water and ammonia. It has been considered as a possible solvent for life by scientists such as Peter Sneath[54] and Carl Sagan.[38]

HF is dangerous to the systems of molecules that Earth-life is made of, but certain other organic compounds, such as paraffin waxes, are stable with it.[38] Like water and ammonia, liquid hydrogen fluoride supports an acid-base chemistry. Using a solvent system definition of acidity and basicity, nitric acid functions as a base when it is added to liquid HF.[55]

However, hydrogen fluoride, unlike water, ammonia and methane, is cosmically rare.[56]

Hydrogen sulfide is the closest chemical analog to water,[57] but is less polar and a weaker inorganic solvent.[58] Hydrogen sulfide is quite plentiful on Jupiter's moon Io, and may be in liquid form a short distance below the surface; and astrobiologist Dirk Schulze-Makuch has suggested it as a possible solvent for life there.[59] On a planet with hydrogen-sulfide oceans the source of the hydrogen sulfide could come from volcanos, in which case it could be mixed in with a bit of hydrogen fluoride, which could help dissolve minerals. Hydrogen sulfide life might use a mixture of carbon monoxide and carbon dioxide as their carbon source. They might produce and live off of sulfur monoxide, which is analogous to oxygen (O2). Hydrogen sulfide, like hydrogen cyanide and ammonia, suffers from the small temperature range where it is liquid, though that, like that of hydrogen cyanide and ammonia, increases with increasing pressure.

Silicon dioxide, also known as glass, silica, or quartz, is very abundant in the universe and has a large temperature range where it is liquid. However, its melting point is 1,600 to 1,725C (2,912 to 3,137F), so it would be impossible to make organic compounds in that temperature, because all of them would decompose. Moreover, if the pressure increases, the melting point goes down.[citation needed] Silicates are similar to silicon dioxide and some could have lower boiling points than silica. Gerald Feinberg and Robert Shapiro have suggested that molten silicate rock could serve as a liquid medium for organisms with a chemistry based on silicon, oxygen, and other elements such as aluminum.[60]

Other solvents sometimes proposed:

Sulfuric acid in liquid form is strongly polar. It remains liquid at higher temperatures than water, its liquid range being 10C to 337C at a pressure of 1 atm, although above 300C it will slowly decompose. Sulfuric acid is known to be abundant in the clouds of Venus, in the form of aerosol droplets. In a biochemistry that used sulfuric acid as a solvent, the alkene group (C=C), with two carbon atoms joined by a double bond, could function analogously to the carbonyl group (C=O) in water-based biochemistry.[33]

A proposal has been made that life on Mars may exist and be using a mixture of water and hydrogen peroxide as its solvent.[64] A 61.2% (by weight) mix of water and hydrogen peroxide has a freezing point of 56.5C, and also tends to super-cool rather than crystallize. It is also hygroscopic, an advantage in a water-scarce environment.[65][66]

Supercritical carbon dioxide has been proposed as a candidate for alternative biochemistry due to its ability to selectively dissolve organic compounds and assist the functioning of enzymes and because "super-Earth"- or "super-Venus"-type planets with dense high-pressure atmospheres may be common.[61]

Physicists have noted that, although photosynthesis on Earth generally involves green plants, a variety of other-colored plants could also support photosynthesis, essential for most life on Earth, and that other colors might be preferred in places that receive a different mix of stellar radiation than Earth.[67][68] These studies indicate that, although blue photosynthetic plants would be less likely, yellow or red plants are plausible.[68]

Many Earth plants and animals undergo major biochemical changes during their life cycles as a response to changing environmental conditions, for example, by having a spore or hibernation state that can be sustained for years or even millennia between more active life stages.[69] Thus, it would be biochemically possible to sustain life in environments that are only periodically consistent with life as we know it.

For example, frogs in cold climates can survive for extended periods of time with most of their body water in a frozen state,[69] whereas desert frogs in Australia can become inactive and dehydrate in dry periods, losing up to 75% of their fluids, yet return to life by rapidly rehydrating in wet periods.[70] Either type of frog would appear biochemically inactive (i.e. not living) during dormant periods to anyone lacking a sensitive means of detecting low levels of metabolism.

In 2007, Vadim N. Tsytovich and colleagues proposed that lifelike behaviors could be exhibited by dust particles suspended in a plasma, under conditions that might exist in space.[71][72] Computer models showed that, when the dust became charged, the particles could self-organize into microscopic helical structures capable of replicating themselves, interacting with other neighboring structures, and evolving into more stable forms. Similar forms of life were described in Fred Hoyle's classic novel The Black Cloud.

Scientists who have considered possible alternatives to carbon-water biochemistry include:

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