Biochemistry

Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms.[1] Biochemical processes give rise to the complexity of life.

A sub-discipline of both biology and chemistry, biochemistry can be divided in three fields; molecular genetics, protein science and metabolism. Over the last decades of the 20th century, biochemistry has through these three disciplines become successful at explaining living processes. Almost all areas of the life sciences are being uncovered and developed by biochemical methodology and research.[2] Biochemistry focuses on understanding how biological molecules give rise to the processes that occur within living cells and between cells,[3] which in turn relates greatly to the study and understanding of tissues, organs, and organism structure and function.[4]

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.[5]

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.[6] 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.[7] 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 diseases.[8] In nutrition, they study how to maintain health wellness and study the effects of nutritional deficiencies.[9] In agriculture, biochemists investigate soil and fertilizers, and try to discover ways to improve crop cultivation, crop storage and pest control.

History

Gerty Theresa Radnitz Cori (1896-1957) and Carl Ferdinand Cori
Gerty Cori and Carl Cori jointly won the Nobel Prize in 1947 for their discovery of the Cori cycle at RPMI.

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, in this sense the history of biochemistry may therefore go back as far as the ancient Greeks.[10] However, biochemistry as a specific scientific discipline has its beginning sometime 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,[11] 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.[12][13] 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,[10] or even earlier to the 18th century studies on fermentation and respiration by Antoine Lavoisier.[14][15] 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,[16] and F. Gowland Hopkins on enzymes and the dynamic nature of biochemistry.[17]

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 für Physiologische Chemie (Journal of Physiological Chemistry) where he argued for the setting up of institutes dedicated to this field of study.[18][19] The German chemist Carl Neuberg however is often cited to have coined the word in 1903,[20][21][22] while some credited it to Franz Hofmeister.[23]

DNA orbit animated
DNA structure (1D65​)[24]

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.[25] Then, in 1828, Friedrich Wöhler published a paper on the synthesis of urea, proving that organic compounds can be created artificially.[26] 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), and led to an understanding of biochemistry on a molecular level. Philip Randle is well known for his discovery in diabetes research is possibly the glucose-fatty acid cycle in 1963.He confirmed that fatty acids reduce oxidation of sugar by the muscle. High fat oxidation was responsible for the insulin resistance.[27]

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.[28] 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.[29] In 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme.[30] In 1988, Colin Pitchfork was the first person convicted of murder with DNA evidence, which led to the growth of forensic science.[31] 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.[32]

Starting materials: the chemical elements of life

201 Elements of the Human Body.02
The main elements that compose the human body are shown from most abundant (by mass) to least abundant.

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 elements—carbon, hydrogen, nitrogen, oxygen, calcium, and phosphorus—make up almost 99% of the mass of living cells, including those in the 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.[33]

Biomolecules

The four main classes of molecules in biochemistry (often called biomolecules) are carbohydrates, lipids, proteins, and nucleic acids.[34] 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.

Carbohydrates

Beta-D-Glucose
Glucose, a monosaccharide
Sucrose-inkscape
A molecule of sucrose (glucose + fructose), a disaccharide
Amylose 3Dprojection.corrected
Amylose, a polysaccharide made up of several thousand glucose units

Two of the main functions of carbohydrates are 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 among 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,[35][a] and deoxyribose (C5H10O4). A monosaccharide can switch between acyclic (open-chain) form and a cyclic form. The open-chain form can be turned into a ring of carbon atoms bridged by an oxygen atom created from the carbonyl group of one end and the hydroxyl group of another. The cyclic molecule has a hemiacetal or hemiketal group, depending on whether the linear form was an aldose or a ketose.[36]

Existence in solution
Conversion between the furanose, acyclic, and pyranose forms of D-glucose

In these cyclic forms, the ring usually has 5 or 6 atoms. These forms are called furanoses and pyranoses, respectively—by analogy with furan and pyran, the simplest compounds with the same carbon-oxygen ring (although they lack the double bonds of these two molecules). For example, the aldohexose glucose may form a hemiacetal linkage between the hydroxyl on carbon 1 and the oxygen on carbon 4, yielding a molecule with a 5-membered ring, called glucofuranose. The same reaction can take place between carbons 1 and 5 to form a molecule with a 6-membered ring, called glucopyranose. Cyclic forms with a 7-atom ring called heptoses are rare.

Two monosaccharides can be joined together by a glycosidic or ether bond into a disaccharide through a dehydration reaction during which a molecule of water is released. The reverse reaction in which the glycosidic bond of a disaccharide is broken into two monosaccharides is termed hydrolysis. The best-known disaccharide is sucrose or ordinary sugar, which consists of a glucose molecule and a fructose molecule joined together. Another important disaccharide is lactose found in milk, consisting of a glucose molecule and a galactose molecule. Lactose may be hydrolysed by lactase, and deficiency in this enzyme results in 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.[37] 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. Cellulose is an important structural component of plant's cell walls and glycogen is 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 forms 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

Common lipids lmaps
Structures of some common lipids. At the top are cholesterol and oleic acid.[38] The middle structure is a triglyceride composed of oleoyl, stearoyl, and palmitoyl chains attached to a glycerol backbone. At the bottom is the common phospholipid, phosphatidylcholine.[39]

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, open chain aliphatic molecules, while others have ring structures. Some are aromatic (with a cyclic [ring] and planar [flat] structure) while others are not. Some are flexible, while others are rigid.[40]

Lipids 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).[41]

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.[42]

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

AminoAcidball
The general structure of an α-amino acid, with the amino group on the left and the carboxyl group on the right.

Proteins are very large molecules—macro-biopolymers—made from monomers called amino acids. An amino acid consists of a carbon atom attached to an amino group, –NH2, a carboxylic acid group, –COOH (although these exist as –NH3+ and –COO under physiologic conditions), a simple hydrogen atom, and a side chain commonly denoted as "–R". The side chain "R" is different for each amino acid of which there are 20 standard ones. It is this "R" group that made 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.[43]

Amino acids 1
Generic amino acids (1) in neutral form, (2) as they exist physiologically, and (3) joined together as a dipeptide.
1GZX Haemoglobin
A schematic of hemoglobin. The red and blue ribbons represent the protein globin; the green structures are the heme groups.

Proteins can have structural and/or functional 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 molecules—they may be extremely selective in what they bind. Antibodies are an example of proteins that attach to one specific type of molecule. Antibodies are composed of heavy and light chains. Two heavy chains would be linked to two light chains through disulfide linkages between their amino acids. Antibodies are specific through variation based on differences in the N-terminal domain.[44]

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. Virtually every reaction in a living cell requires an enzyme to lower the activation energy of the reaction. 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 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 α-helix or into a sheet called a β-sheet; some α-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.[45]

Protein structure examples
Examples of protein structures from the Protein Data Bank
Structural coverage of the human cyclophilin family
Members of a protein family, as represented by the structures of the isomerase domains

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 α-keto acid. Enzymes called transaminases can easily transfer the amino group from one amino acid (making it an α-keto acid) to another α-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 α-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.[46]

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 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.[47]

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.[48] 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

0322 DNA Nucleotides
The structure of deoxyribonucleic acid (DNA), the picture shows the monomers being put together.

Nucleic acids, so called because of their 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.[2] 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.[49]

Nucleotides 1
Structural elements of common nucleic acid constituents. Because they contain at least one phosphate group, the compounds marked nucleoside monophosphate, nucleoside diphosphate and nucleoside triphosphate are all nucleotides (not simply phosphate-lacking nucleosides).

The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).[50] 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.[51] 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.

Metabolism

Carbohydrates as energy source

Glucose is an 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.

Glycolysis (anaerobic)

The image above contains clickable links
The metabolic pathway of glycolysis converts glucose to pyruvate by via a series of intermediate metabolites. Each chemical modification (red box) is performed by a different enzyme. Steps 1 and 3 consume ATP (blue) and steps 7 and 10 produce ATP (yellow). Since steps 6-10 occur twice per glucose molecule, this leads to a net production of ATP.

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 of converting NAD+ (nicotinamide adenine dinucleotide: oxidised form) to NADH (nicotinamide adenine dinucleotide: reduced form). 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.[52]

Aerobic

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 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).[53] 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.

Gluconeogenesis

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.[54]

Relationship to other "molecular-scale" biological sciences

Schematic relationship between biochemistry, genetics and molecular biology
Schematic relationship between biochemistry, genetics, and molecular biology.

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:

  • Biochemistry is the study of the chemical substances and vital processes occurring in living organisms. Biochemists focus heavily on the role, function, and structure of biomolecules. The study of the chemistry behind biological processes and the synthesis of biologically active molecules are examples of biochemistry.
  • Genetics is the study of the effect of genetic differences on organisms. Often this can be inferred by the absence of a normal component (e.g., one gene), in the study of "mutants"—organisms with a changed gene that leads to the organism being different with respect to the so-called "wild type" or normal phenotype. Genetic interactions (epistasis) can often confound simple interpretations of such "knock-out" or "knock-in" studies.
  • Molecular biology is the study of molecular underpinnings of the process of replication, transcription and translation of the genetic material. The central dogma of molecular biology where genetic material is transcribed into RNA and then translated into protein, despite being an oversimplified picture of molecular biology, still provides a good starting point for understanding the field. This picture, however, is undergoing revision in light of emerging novel roles for RNA.[55]
  • Chemical biology seeks to develop new tools based on small molecules that allow minimal perturbation of biological systems while providing detailed information about their function. Further, chemical biology employs biological systems to create non-natural hybrids between biomolecules and synthetic devices (for example emptied viral capsids that can deliver gene therapy or drug molecules).[56]

See also

Lists

See also

Notes

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 24% fructose and 8% sucrose. However, peaches contain more sucrose (6.66%) than they do fructose (0.93%) or glucose (1.47%).[57]

References

  1. ^ "Biochemistry". acs.org.
  2. ^ a b Voet (2005), p. 3.
  3. ^ Karp (2009), p. 2.
  4. ^ Miller (2012). p. 62.
  5. ^ Astbury (1961), p. 1124.
  6. ^ Eldra (2007), p. 45.
  7. ^ Marks (2012), Chapter 14.
  8. ^ Finkel (2009), pp. 1–4.
  9. ^ UNICEF (2010), pp. 61, 75.
  10. ^ a b Helvoort (2000), p. 81.
  11. ^ Hunter (2000), p. 75.
  12. ^ Hamblin (2005), p. 26.
  13. ^ Hunter (2000), pp. 96–98.
  14. ^ Berg (1980), pp. 1–2.
  15. ^ Holmes (1987), p. xv.
  16. ^ Feldman (2001), p. 206.
  17. ^ Rayner-Canham (2005), p. 136.
  18. ^ Ziesak (1999), p. 169.
  19. ^ Kleinkauf (1988), p. 116.
  20. ^ Ben-Menahem (2009), p. 2982.
  21. ^ Amsler (1986), p. 55.
  22. ^ Horton (2013), p. 36.
  23. ^ Kleinkauf (1988), p. 43.
  24. ^ Edwards (1992), pp. 1161–1173.
  25. ^ Fiske (1890), pp. 419–20.
  26. ^ Kauffman (2001), pp. 121–133.
  27. ^ Ashcroft(2006)
  28. ^ Tropp (2012), p. 2.
  29. ^ Tropp (2012), pp. 19–20.
  30. ^ Krebs (2012), p. 32.
  31. ^ Butler (2009), p. 5.
  32. ^ Chandan (2007), pp. 193–194.
  33. ^ Nielsen (1999), pp. 283–303.
  34. ^ Slabaugh (2007), pp. 3–6.
  35. ^ Whiting (1970), pp. 1–31.
  36. ^ Voet (2005), pp. 358–359.
  37. ^ Varki (1999), p. 17.
  38. ^ Stryer (2007), p. 328.
  39. ^ Voet (2005), Ch. 12 Lipids and Membranes.
  40. ^ Fromm and Hargrove (2012), pp. 22–27.
  41. ^ Voet (2005), pp. 382–385.
  42. ^ Voet (2005), pp. 385–389.
  43. ^ Metzler (2001), p. 58.
  44. ^ Feige, Matthias J.; Hendershot, Linda M.; Buchner, Johannes (2010). "How antibodies fold". Trends in Biochemical Sciences. 35 (4): 189–198. doi:10.1016/j.tibs.2009.11.005. PMC 4716677. PMID 20022755.
  45. ^ Fromm and Hargrove (2012), pp. 35–51.
  46. ^ Fromm and Hargrove (2012), pp. 279–292.
  47. ^ Sherwood (2012), p. 558.
  48. ^ Fariselli (2007), pp. 78–87.
  49. ^ Saenger (1984), p. 84.
  50. ^ Tropp (2012), pp. 5–9.
  51. ^ Knowles (1980), pp. 877–919.
  52. ^ Fromm and Hargrove (2012), pp. 163–180.
  53. ^ Voet (2005), Ch. 17 Glycolysis.
  54. ^ Fromm and Hargrove (2012), pp. 183–194.
  55. ^ Ulveling (2011), pp. 633–644.
  56. ^ Rojas-Ruiz (2011), pp. 2672–2687.
  57. ^ Whiting, G.C. (1970), p. 5.

Cited literature

Further reading

External links

Poirot, Marc; Soules, Regis; Mallinger, Arnaud; Dalenc, Florence; Silvente-Poirot, Sandrine. Biochimie. Oct2018, Vol. 153, pp. 139–149 Afify, Heba M. American Journal of Biomedical Sciences. 2016, Vol. 8 Issue 3, pp. 200–207

Biochemist

Biochemists are scientists that are trained in biochemistry.

Biomolecule

A biomolecule or biological molecule is a loosely used term for molecules and ions that are present in organisms, essential to some typically biological process such as cell division, morphogenesis, or development. Biomolecules include large macromolecules (or polyanions) such as proteins, carbohydrates, lipids, and nucleic acids, as well as small molecules such as primary metabolites, secondary metabolites, and natural products. A more general name for this class of material is biological materials. Biomolecules are usually endogenous but may also be exogenous. For example, pharmaceutical drugs may be natural products or semisynthetic (biopharmaceuticals) or they may be totally synthetic.

Biology and its subsets of biochemistry and molecular biology study biomolecules and their reactions. Most biomolecules are organic compounds, and just four elements—oxygen, carbon, hydrogen, and nitrogen—make up 96% of the human body's mass. But many other elements, such as the various biometals, are present in small amounts.

The uniformity of specific types of molecules (the biomolecules) and of some metabolic pathways as invariant features between the diversity of life forms is called "biochemical universals" or "theory of material unity of the living beings", a unifying concept in biology, along with cell theory and evolution theory.

Biophysics

Biophysics is an interdisciplinary science that applies approaches and methods traditionally used in physics to study biological phenomena. Biophysics covers all scales of biological organization, from molecular to organismic and populations. Biophysical research shares significant overlap with biochemistry, molecular biology, physical chemistry, physiology, nanotechnology, bioengineering, computational biology, biomechanics, developmental biology and systems biology.

The term biophysics was originally introduced by Karl Pearson in 1892. Ambiguously, the term biophysics is also regularly used in academia to indicate the study of the physical quantities (e.g. electric current, temperature, stress, entropy) in biological systems, which is, by definition, performed by physiology. Nevertheless, other biological sciences also perform research on the biophysical properties of living organisms including molecular biology, cell biology, biophysics, and biochemistry.

Clinical chemistry

Clinical chemistry (also known as chemical pathology, clinical biochemistry or medical biochemistry) is the area of chemistry that is generally concerned with analysis of bodily fluids for diagnostic and therapeutic purposes. It is an applied form of biochemistry (not to be confused with medicinal chemistry, which involves basic research for drug development).

The discipline originated in the late 19th century with the use of simple chemical reaction tests for various components of blood and urine. In the many decades since, other techniques have been applied as science and technology have advanced, including the use and measurement of enzyme activities, spectrophotometry, electrophoresis, and immunoassay. There are now many blood tests and clinical urine tests with extensive diagnostic capabilities.

Most current laboratories are now highly automated to accommodate the high workload typical of a hospital laboratory. Tests performed are closely monitored and quality controlled.

All biochemical tests come under chemical pathology. These are performed on any kind of body fluid, but mostly on serum or plasma. Serum is the yellow watery part of blood that is left after blood has been allowed to clot and all blood cells have been removed. This is most easily done by centrifugation, which packs the denser blood cells and platelets to the bottom of the centrifuge tube, leaving the liquid serum fraction resting above the packed cells. This initial step before analysis has recently been included in instruments that operate on the "integrated system" principle. Plasma is in essence the same as serum, but is obtained by centrifuging the blood without clotting. Plasma is obtained by centrifugation before clotting occurs. The type of test required dictates what type of sample is used.

A large medical laboratory will accept samples for up to about 700 different kinds of tests. Even the largest of laboratories rarely do all these tests themselves, and some must be referred to other labs.

This large array of tests can be categorised into sub-specialities of:

General or routine chemistry – commonly ordered blood chemistries (e.g., liver and kidney function tests).

Special chemistry - elaborate techniques such as electrophoresis, and manual testing methods.

Clinical endocrinology – the study of hormones, and diagnosis of endocrine disorders.

Toxicology – the study of drugs of abuse and other chemicals.

Therapeutic Drug Monitoring – measurement of therapeutic medication levels to optimize dosage.

Urinalysis – chemical analysis of urine for a wide array of diseases, along with other fluids such as CSF and effusions

Fecal analysis – mostly for detection of gastrointestinal disorders.

Cofactor (biochemistry)

A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme's activity. Cofactors can be considered "helper molecules" that assist in biochemical transformations. The rates at which these happen are characterized by enzyme kinetics.

Cofactors can be subclassified as either inorganic ions or complex organic molecules called coenzymes, the latter of which is mostly derived from vitamins and other organic essential nutrients in small amounts. A coenzyme that is tightly or even covalently bound is termed a prosthetic group. Cosubstrates are transiently bound to the protein and will be released at some point, then get back in. The prosthetic groups, on the other hand, are bound permanently to the protein. Both of them have the same function, which is to facilitate the reaction of enzymes and protein. Additionally, some sources also limit the use of the term "cofactor" to inorganic substances. An inactive enzyme without the cofactor is called an apoenzyme, while the complete enzyme with cofactor is called a holoenzyme.Some enzymes or enzyme complexes require several cofactors. For example, the multienzyme complex pyruvate dehydrogenase at the junction of glycolysis and the citric acid cycle requires five organic cofactors and one metal ion: loosely bound thiamine pyrophosphate (TPP), covalently bound lipoamide and flavin adenine dinucleotide (FAD), and the cosubstrates nicotinamide adenine dinucleotide (NAD+) and coenzyme A (CoA), and a metal ion (Mg2+).Organic cofactors are often vitamins or made from vitamins. Many contain the nucleotide adenosine monophosphate (AMP) as part of their structures, such as ATP, coenzyme A, FAD, and NAD+. This common structure may reflect a common evolutionary origin as part of ribozymes in an ancient RNA world. It has been suggested that the AMP part of the molecule can be considered to be a kind of "handle" by which the enzyme can "grasp" the coenzyme to switch it between different catalytic centers.

ExPASy

ExPASy is a bioinformatics resource portal operated by the SIB Swiss Institute of Bioinformatics and in particular the SIB Web Team. It is an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can access a wide range of resources in many different domains, such as proteomics, genomics, phylogenetics/evolution, systems biology, population genetics, and transcriptomics. The individual resources (databases, web-based and downloadable software tools) are hosted in a decentralised way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by many different SIB groups and external institutions. The portal features a search function across selected resources. Internally, the availability and usage of resources are monitored. The portal is aimed for both expert users and for people who are not familiar with a specific domain in life sciences: in particular, the new web interface provides visual guidance for newcomers to ExPASy.

Fermentation

Fermentation is a metabolic process that produces chemical changes in organic substrates through the action of enzymes. In biochemistry, it is narrowly defined as the extraction of energy from carbohydrates in the absence of oxygen. In the context of food production, it may more broadly refer to any process in which the activity of microorganisms brings about a desirable change to a foodstuff or beverage. The science of fermentation is known as zymology.

In microorganisms, fermentation is the primary means of producing ATP by the degradation of organic nutrients anaerobically. Humans have used fermentation to produce foodstuffs and beverages since the Neolithic age. For example, fermentation is used for preservation in a process that produces lactic acid found in such sour foods as pickled cucumbers, kimchi, and yogurt, as well as for producing alcoholic beverages such as wine and beer. Fermentation occurs within the gastrointestinal tracts of all animals, including humans.

IntEnz

IntEnz (Integrated relational Enzyme database) contains data on enzymes organized by enzyme EC number and is the official version of the Enzyme Nomenclature system developed by the International Union of Biochemistry and Molecular Biology.

Ligand (biochemistry)

In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. The binding typically results in a change of conformational isomerism (conformation) of the target protein. In DNA-ligand binding studies, the ligand can be a small molecule, ion, or protein which binds to the DNA double helix. The relationship between ligand and binding partner is a function of charge, hydrophobicity, and molecular structure. The instance of binding occurs over an infinitesimal range of time and space, so the rate constant is usually a very small number.

Binding occurs by intermolecular forces, such as ionic bonds, hydrogen bonds and Van der Waals forces. The association of docking is actually reversible through dissociation. Measurably irreversible covalent bonding between a ligand and target molecule is atypical in biological systems. In contrast to the definition of ligand in metalorganic and inorganic chemistry, in biochemistry it is ambiguous whether the ligand generally binds at a metal site, as is the case in hemoglobin. In general, the interpretation of ligand is contextual with regards to what sort of binding has been observed. The etymology stems from ligare, which means 'to bind'.

Ligand binding to a receptor protein alters the conformation by affecting the three-dimensional shape orientation. The conformation of a receptor protein composes the functional state. Ligands include substrates, inhibitors, activators, and neurotransmitters. The rate of binding is called affinity, and this measurement typifies a tendency or strength of the effect. Binding affinity is actualized not only by host–guest interactions, but also by solvent effects that can play a dominant, steric role which drives non-covalent binding in solution. The solvent provides a chemical environment for the ligand and receptor to adapt, and thus accept or reject each other as partners.

Radioligands are radioisotope labeled compounds used in vivo as tracers in PET studies and for in vitro binding studies.

Pharmacology

Pharmacology is the branch of biology concerned with the study of drug action, where a drug can be broadly defined as any man-made, natural, or endogenous (from within the body) molecule which exerts a biochemical or physiological effect on the cell, tissue, organ, or organism (sometimes the word pharmacon is used as a term to encompass these endogenous and exogenous bioactive species). More specifically, it is the study of the interactions that occur between a living organism and chemicals that affect normal or abnormal biochemical function. If substances have medicinal properties, they are considered pharmaceuticals.

The field encompasses drug composition and properties, synthesis and drug design, molecular and cellular mechanisms, organ/systems mechanisms, signal transduction/cellular communication, molecular diagnostics, interactions, toxicology, chemical biology, therapy, and medical applications and antipathogenic capabilities. The two main areas of pharmacology are pharmacodynamics and pharmacokinetics. Pharmacodynamics studies the effects of a drug on biological systems, and Pharmacokinetics studies the effects of biological systems on a drug. In broad terms, pharmacodynamics discusses the chemicals with biological receptors, and pharmacokinetics discusses the absorption, distribution, metabolism, and excretion (ADME) of chemicals from the biological systems. Pharmacology is not synonymous with pharmacy and the two terms are frequently confused. Pharmacology, a biomedical science, deals with the research, discovery, and characterization of chemicals which show biological effects and the elucidation of cellular and organismal function in relation to these chemicals. In contrast, pharmacy, a health services profession, is concerned with application of the principles learned from pharmacology in its clinical settings; whether it be in a dispensing or clinical care role. In either field, the primary contrast between the two are their distinctions between direct-patient care, for pharmacy practice, and the science-oriented research field, driven by pharmacology.

The origins of clinical pharmacology date back to the Middle Ages in Avicenna's The Canon of Medicine, Peter of Spain's Commentary on Isaac, and John of St Amand's Commentary on the Antedotary of Nicholas. Clinical pharmacology owes much of its foundation to the work of William Withering. Pharmacology as a scientific discipline did not further advance until the mid-19th century amid the great biomedical resurgence of that period. Before the second half of the nineteenth century, the remarkable potency and specificity of the actions of drugs such as morphine, quinine and digitalis were explained vaguely and with reference to extraordinary chemical powers and affinities to certain organs or tissues. The first pharmacology department was set up by Rudolf Buchheim in 1847, in recognition of the need to understand how therapeutic drugs and poisons produced their effects.Early pharmacologists focused on natural substances, mainly plant extracts. Pharmacology developed in the 19th century as a biomedical science that applied the principles of scientific experimentation to therapeutic contexts. Today pharmacologists use genetics, molecular biology, biochemistry, and other advanced tools to transform information about molecular mechanisms and targets into therapies directed against disease, defects or pathogens, and create methods for preventative care, diagnostics, and ultimately personalized medicine.

Plant physiology

Plant physiology is a subdiscipline of botany concerned with the functioning, or physiology, of plants. Closely related fields include plant morphology (structure of plants), plant ecology (interactions with the environment), phytochemistry (biochemistry of plants), cell biology, genetics, biophysics and molecular biology.

Fundamental processes such as photosynthesis, respiration, plant nutrition, plant hormone functions, tropisms, nastic movements, photoperiodism, photomorphogenesis, circadian rhythms, environmental stress physiology, seed germination, dormancy and stomata function and transpiration, both parts of plant water relations, are studied by plant physiologists.

Precursor (chemistry)

In chemistry, a precursor is a compound that participates in a chemical reaction that produces another compound.

In biochemistry, the term "precursor" often refers more specifically to a chemical compound preceding another in a metabolic pathway, such as a protein precursor.

Product (chemistry)

Products are the species formed from chemical reactions. During a chemical reaction reactants are transformed into products after passing through a high energy transition state. This process results in the consumption of the reactants. It can be a spontaneous reaction or mediated by catalysts which lower the energy of the transition state, and by solvents which provide the chemical environment necessary for the reaction to take place. When represented in chemical equations products are by convention drawn on the right-hand side, even in the case of reversible reactions. The properties of products such as their energies help determine several characteristics of a chemical reaction such as whether the reaction is exergonic or endergonic. Additionally the properties of a product can make it easier to extract and purify following a chemical reaction, especially if the product has a different state of matter than the reactants. Reactants are molecular materials used to create chemical reactions. The atoms aren't created or destroyed. The materials are reactive and reactants are rearranging during a chemical reaction. Here is an example of reactants: CH4 + O2. A non-example is CO2 + H2O or "energy".

Much of chemistry research is focused on the synthesis and characterization of beneficial products, as well as the detection and removal of undesirable products. Synthetic chemists can be subdivided into research chemists who design new chemicals and pioneer new methods for synthesizing chemicals, as well as process chemists who scale up chemical production and make it safer, more environmentally sustainable, and more efficient. Other fields include natural product chemists who isolate products created by living organisms and then characterize and study these products.

Protein dimer

In biochemistry, a protein dimer is a macromolecular complex formed by two protein monomers, or single proteins, which are usually non-covalently bound. Many macromolecules, such as proteins or nucleic acids, form dimers. The word dimer has roots meaning "two parts", di- + -mer. A protein dimer is a type of protein quaternary structure.

A protein homodimer is formed by two identical proteins. A protein heterodimer is formed by two different proteins.

Most protein dimers in biochemistry are not connected by covalent bonds. An example of a non-covalent heterodimer is the enzyme reverse transcriptase, which is composed of two different amino acid chains. An exception is dimers that are linked by disulfide bridges such as the homodimeric protein NEMO.Some proteins contain specialized domains to ensure dimerization (dimerization domains) and specificity.

Putrefaction

Putrefaction is the fifth stage of death, following pallor mortis, algor mortis, rigor mortis, and livor mortis. This process references the breaking down of a body of a human or animal post-mortem (meaning after death). In broad terms, it can be viewed as the decomposition of proteins, and the eventual breakdown of the cohesiveness between tissues, and the liquefaction of most organs. This is caused by the decomposition of organic matter by bacterial or fungal digestion, which causes the release of gases that infiltrate the body's tissues, and leads to the deterioration of the tissues and organs.

The approximate time it takes putrefaction to occur is dependent on various factors. Internal factors that affect the rate of putrefaction include the age at which death has occurred, the overall structure and condition of the body, the cause of death, and external injuries arising before or after death. External factors include environmental temperature, moisture and air exposure, clothing, burial factors, and light exposure.

The first signs of putrefaction are signified by a greenish discoloration on the outside of the skin on the abdominal wall corresponding to where the large intestine begins, as well as under the surface of the liver.

Certain substances, such as carbolic acid, arsenic, strychnine, and zinc chloride, can be used to delay the process of putrefaction in various ways based on their chemical make up.

Body farms are facilities which study the process of human decomposition as well as how environmental factors affect the rate of putrefaction.

Receptor (biochemistry)

In biochemistry and pharmacology, a receptor is a protein molecule that receives chemical signals from outside a cell. When such chemical signals bind to a receptor, they cause some form of cellular/tissue response, e.g. a change in the electrical activity of a cell. There are three main ways the action of the receptor can be classified: relay of signal, amplification, or integration. Relaying sends the signal onward, amplification increases the effect of a single ligand, and integration allows the signal to be incorporated into another biochemical pathway. In this sense, a receptor is a protein-molecule that recognizes and responds to endogenous chemical signals, e.g. an acetylcholine receptor recognizes and responds to its endogenous ligand, acetylcholine. However, sometimes in pharmacology, the term is also used to include other proteins that are drug targets, such as enzymes, transporters, and ion channels.

Receptor proteins can be classified by their location. Transmembrane receptors include ion channel-linked (ionotropic) receptors, G protein-linked (metabotropic) hormone receptors, and enzyme-linked hormone receptors. Intracellular receptors are those found inside the cell, and include cytoplasmic receptors and nuclear receptors. A molecule that binds to a receptor is called a ligand, and can be a protein or peptide (short protein), or another small molecule such as a neurotransmitter, hormone, pharmaceutical drug, toxin, or parts of the outside of a virus or microbe. The endogenously designated -molecule for a particular receptor is referred to as its endogenous ligand. E.g. the endogenous ligand for the nicotinic acetylcholine receptor is acetylcholine but the receptor can also be activated by nicotine and blocked by curare.Each receptor is linked to a specific cellular biochemical pathway. While numerous receptors are found in most cells, each receptor will only bind with ligands of a particular structure, much like how locks will only accept specifically shaped keys. When a ligand binds to its corresponding receptor, it activates or inhibits the receptor's associated biochemical pathway.

Residue (chemistry)

In chemistry residue is whatever remains or acts as a contaminant after a given class of events.

Residue may be the material remaining after a process of preparation, separation, or purification, such as distillation, evaporation, or filtration. It may also denote the undesired by-products of a chemical reaction.

Science Citation Index

The Science Citation Index (SCI) is a citation index originally produced by the Institute for Scientific Information (ISI) and created by Eugene Garfield. It was officially launched in 1964. It is now owned by Clarivate Analytics (previously the Intellectual Property and Science business of Thomson Reuters). The larger version (Science Citation Index Expanded) covers more than 8,500 notable and significant journals, across 150 disciplines, from 1900 to the present. These are alternatively described as the world's leading journals of science and technology, because of a rigorous selection process.The index is made available online through different platforms, such as the Web of Science and SciSearch. (There are also CD and printed editions, covering a smaller number of journals). This database allows a researcher to identify which later articles have cited any particular earlier article, or have cited the articles of any particular author, or have been cited most frequently. Thomson Reuters also markets several subsets of this database, termed "Specialty Citation Indexes", such as the Neuroscience Citation Index and the Chemistry Citation Index.

Substrate (chemistry)

In chemistry, a substrate is typically the chemical species being observed in a chemical reaction, which reacts with a reagent to generate a product. In synthetic and organic chemistry, the substrate is the chemical of interest that is being modified. In biochemistry, an enzyme substrate is the material upon which an enzyme acts. When referring to Le Chatelier's principle, the substrate is the reagent whose concentration is changed. The term substrate is highly context-dependent. It essentially refers to the part of the molecule that is precursor to a product.

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