Biochemistry

The biochemistry is the scientific discipline which studies the chemical reactions taking place within the cell S.

The term was created in 1903 by Carl Neuberg according to the Greek root Βιοχημεία (biochēmeia). One distinguishes several great subdivisions from this discipline: the energy , production of energy by the cell; the enzymology, or study of the biological Catalyst S; the Metabolism, divided into Anabolism, reaction of synthesis of molecules and Catabolism, reactions of degradations of the molecule.
Ces great groups are subdivided then in increasingly specialized fields. For example, the modern enzymology stains to connect the three-dimensional structure of a protein with its function. Biochemistry, just like chemistry, detail also the reasons of the reactivity of the molecules.

The principal categories of molecules studied in biochemistry are the Glucide S, the Lipide S, the Protéine S and the nucleic acid. These molecules are made up mainly of carbon, oxygen and nitrogen. These classes of molecules represent the basic elements of the construction and the operation of the cell.

One of the goals ultimate of biochemistry is to integrate the data obtained into the molecular scales on a higher level of complexity, that of the cell. There exist however two divisions between the molecule and the cell: first is approached by the Biochimie supramoléculaire, which studies the assemblies of Macromolécule S (like the Ribosome or the interactions enzymatic within a metabolic Voie) and the emergent properties; the second deals with biochemistry of the Organelle S, like the Mitochondrie or the Chloroplaste, entities supramoléculaires existing inside the complex cells.

Emergence of biochemistry

See also: History of biology

The idea that the activity of the " living matter " comes from chemical reactions is relatively old (Réaumur, Spallanzani, etc). The synthesis of the Urea, realized in 1828 by the German chemist Friedrich Wöhler, will be one of the most decisive confirmations carried out with. Before this date, one considered that the substance present in the organizations presented characteristics suitable for alive (theory of the Vitalisme or Humeur S inherited the old Greeks Aristote, Gallien or Hippocrates).

Another German, Justus von Liebig will be the promoter of a new science, biochemistry, which will be a field of illustration for several of its compatriots until the second world war. Among most famous one will retain Hermann Emil Fischer (projection of Fischer of glucids celebrates it), Eduard Buchner (biochemistry of fermentation) and Richard Willstätter (mechanism of the enzymatic reactions).

Consequently the exploration of the cell makes new great strides but one will be interested more particularly in his chemical components and the way in which they react between them in order to carry out a Métabolisme at the cellular level. After work of Louis Pasteur, research will go in the substances intervening in the Fermentation S and the Digestion S (soluble leavens). Antoine Béchamp will name them in 1864 " zymases" but one will prefer to use the name of Enzymes introduces since 1878 by Wilhelm Kühne.

The other components drawing the attention are molecules " albuminoïdes" named Proteins since 1838. Those if are regarded as aggregates of small molecules at the origin of the colloidal state of the Hyaloplasme of the cell. According to Friedrich Engels they are the demonstration even of the life (Dialectical of nature, 1835), that consequently generates a vitalistic attitude which in France will be defended by Emile Duclaux. However, since 1920, another interpretation is essential with the description of the molecular nature of proteins by Hermann Staudinger. This new statute is accompanied by structural characteristics which lead to new functional interpretations, certain proteins being able to be enzymes, as Victor Henri had had a presentiment of it since 1903.

Otto Warburg sets up cellular chemistry and places the microrespirometer at the disposal of the researchers. This apparatus will help the Hungarian Albert Szent-Györgyi then the German Hans Adolf Krebs to elucidate the mechanism of cellular breathing. It is shown whereas the carbonic gas produced on this occasion is the result of a series of biochemical reactions carried out using specific enzymes, the Cycle of Krebs. One also establishes that all the cells draw their energy from the same molecule, adenosine triphosphate or ATP, discovered in 1929 by Karl Lohmann.

With beginning of the year 40, Albert Claude watch which the synthesis of the ATP proceeds on the level of the internal membrane of the Mitochondries. In same time, the British Peter Mitchell explains the mechanism of this reaction, which is accompanied by the water formation.

The study of the Thylakoïde S in the Chloroplaste S of the chlorophyllian plants makes it possible to include/understand the mechanism of photosynthesis gradually. In 1932, Robert Emerson recognizes a luminous phase and an obscure phase and in 1937 Archibald Vivian Hill shows that the production of oxygen characteristic of the Photosynthèse results from the photolysis (chemical decomposition by the light) from water. Finally as from 1947, Melvin Calvin describes the manufacture of the carbonaceous substances starting from absorptive carbon dioxide, it is the Cycle of Calvin.

In 1951, Erwin Chargaff watch that the molecule of DNA, known since 1869, is primarily present at the level of the Chromosome S. One notices also which there is as many Adénine that of Thymine, of Guanine that of Cytosine). The young person James Dewey Watson and Francis Harry Compton Crick will publish the structure in double helix of the DNA in the review Nature on April 25th, 1953. They base on the images in diffraction of x-rays obtained by Maurice Wilkins and Rosalind Elsie Franklin.

All these discoveries are the prelude to a better molecular comprehension of the life and to many others medical and biological projections.

Appearance of the techniques of biochemistry

It is into 1929 that Theodor Svedberg with the idea to subject the cellular material to a thorough Centrifugation (ultracentrifugation) in order to isolate the various components from the cells. In 1906, the botanist Mikhaïl Tswett develops the Chromatographie, technique allowing to separate the biomolécules. The technique of electrophoresis was developed in 1930 by Arne Wilhelm Tiselius, it allows the separation of the biomolécules charged under the effect of an electric field. The British biochemist Frederick Sanger developed in 1955 a new method to analyze the molecular structure of the proteins (sequence of amino-acids) and showed that a molecule of Insuline contained two peptide chains, connected together by two bridges disulfide.

. From a metabolic point of view, the lipids constitute energy reserves. Sugars for example are transformed into lipids and are stored in the fat cells in the event of consumption higher than the use.
Les lipids, in particular the Phospholipide S constitute the major element of the cellular membranes. They define a separation between the intracellular medium and the extracellular medium. Their hydrophobic character makes impossible the passage of molecules polar or charged, like water and the ions. Only ways of possible passage: the membrane proteins. for example, the ions enter and leave the cells by the means of channels ionic.
Plusieurs Hormone S are lipids, in general derived from the Cholestérol: Progesterone, Testosterone, etc the Vitamine S liposoluble can also be classified among the lipids.

Contrary to the nucleic acid or the Protein S, the lipids are not macromolecules made up of a succession of units of bases.

Structure and classification

The lipids can be classified according to the structure of their carbonaceous Squelette (carbon atoms chained, cyclic, presence of non-saturations, etc ):

  • the fatty-acids: it acts of carboxylic acid with long carbonaceous chain being able to be saturated, unsaturated, ramified, etc . Well-known examples are the Omega-3 and -6, but also the Prostaglandine S.

  • the Acylglycérol S and Phosphoacylglycérol S: these lipids are formed by Estérification of a Glycérol and of one to three fatty-acids (or mono, di- and triglycerides). In the case of the phosphoacylglycérols, esterification is done with glycerol, a or two fatty-acids and a Phosphate. the phosphate group can in its turn undergo an esterification by different hydroxylated compounds like the Choline or the Sérine. One then obtains phosphatidylcholine and phosphatidylsérine, respectively. It is it should be noted that acylglycérols and phosphoacylglycérols are also known under the names of glycérides and phosphoglycérides.

  • the Sphingolipide S: these lipids result from the Estérification then of the amide formation of serine by two fatty-acids. A well-known subclass of sphingolipides is that of the céramides.

  • the Sterol S: sterols are lipids having a cyclized carbonaceous chain several times. They are thus not linear like the fatty-acids. Well-known examples of sterols are the Cholestérol, the Vitamine D and the hormones stéroïdiennes (Testostérone, estrogen S, Cortisone).

  • the Prénol S: it acts of lipids deriving from the Isoprène, such as for example the vitamins E and K or the β-carotene

  • the Polykétide S: they form a very vast range of natural compounds from which are derived from many antibiotics like the Macrolide S

  • the Saccharolipide S: they result from the Estérification and/or the amide formation of sugars and fatty-acids. The most known example of saccharolipide is undoubtedly the Lipopolysaccharide.

For practical and historical reasons, Acylglycérol and Phosphoacylglycérol are often regarded as two different categories, just as Phosphoacylglycérol and phosphosphingolipide can be gathered under the phospholipide name

Some examples of lipids , one estimates at a different million the number of Protéine S which can be produced in the human cells (Protéome). The number of proteins produced by the human Cerveau, whose role is essential for its operation, is estimated at approximately 12  000.

Nucleic acids

See also: Nucleic acid

The nucleic acid were isolated initially from the cores of the cells Eucaryote S (of Latin nucleus , core). They are Macromolécule S comprising of the sub-units called Nucléotide S. One can distinguish two great types from them: desoxyribonucleic acid (DNA) and ribonucleic acid (ARN). DNA is the universal support of the genetic information (except for some Virus). Thanks to two catalytic functions this molecule ensures the transmission and the expression of the information which it contains:

  • the autocatalytic function: the autoduplication DNA allows and ensures the transmission of the information of a generation another.
  • the heterocatalytic function: control the proteinic synthesis. Since the Enzyme S are Protéine S and that all the syntheses and reactions depend on them, DNA control all the biological organization and processes of the cell S and the organization S. Ainsi, DNA expresses the information which it includes/understands.

Structure

The Nucleotide, unit basic nucleic acid, comprises three components: phosphoric Acid , a Pentose and a nitrogenized Base:

  • the phosphoric Acid (H3PO4) has 3 functions Acide S. Two of these functions are esterified by two functions alcohol S carried by carbons 3 ' and 5 ' of the Pentose. The third acid function is free. (One numbers carbons with figures accompanied by the indication (') to avoid confusions with classifications of the bases).

  • the Pentose (sugar in C5): It is the Ribose, present in two forms the 2 ' - désoxyribose and 2 ' - oxyribose respectively in DNA and ARN. The connection Pentose - base is a glycosidic Liaison. It is formed by elimination of a water molecule between the base and the semi-acetal OH located on carbon 1 ' of the ose. Association Pentose - base is called Nucléoside.

  • the nitrogenized bases are classified in pyrimidic bases and purine bases. The principal pyrimidic bases are: the Uracil (U), the Cytosine (C) and the Thymine (T). The principal purine bases are: the Adénine (A) and the Guanine (G). The purine and pyrimidic bases present interconvertibles chemical forms which one calls of the forms Tautomère S.

In DNA bincaténaire the bases nitrogenized of the two bits are paired according to the Règle of complementarity: With paired with T, C paired with G. This pairing is maintained thanks to hydrogen bonds and can be thus affected by heat (thermal denaturation). By convention, the sequence of a Nucleic acid is directed in the direction of end 5 ' (comprising a grouping phosphates) towards the end 3 ' which has a free OH. Thus, in DNA bincaténaire (double bit), the two bits are laid out in two opposite directions. Ends 5 ' and 3 ' of the one of the bits correspond at ends 3 ' and 5 ' of the opposite parallel bit (Anti-parallèle S). In space the two chains present a helicoid configuration. They are rolled up around a secondary axis to constitute a double right rotating helix (in the forms has and B of DNA) or more exceptionally rotating left (in the form Z of DNA).

Genetic information

Classically, it is considered that the Gène is an area of a bit of DNA whose sequence codes the necessary information with the synthesis of Protéine. Three different types of DNA constitute the Génome (the whole of genes of an individual or a Espèce):

  • “domestic” DNA: accounting for approximately 75% of the Genome, is made of Gène S present in only one specimen or a limited number of copies. However, by extension this type of DNA includes also certain genes specific known as to multicopies, like those of ribosomal ARN or those coding the Histone S. The latter exist in the form of broad clusters of copies (50-10 000 copies) localized on one or more Chromosome S.
  • “repetitive and dispersed” DNA (Minisatellite S and Microsatellite S): constitute 15% of the genome and is characterized by short nucleotidic sequences (higher than 100 for the minis) repeated out of tandem a very great number of times (10
>5 - 106 time) in many areas of the Genome.
  • “satellite” DNA: (approximately 10  % of the Génome) consists of highly repetitive sequences, primarily localized in the areas of the Centromère S and the Télomère S.

The Human genome includes/understands approximately 3 billion pairs of Nucléotide S representing nearly 30.000 Gène S (in made, for the recent estimates it is between 20.000 and 25.000 genes). However, there does not seem to be systematic relation between the number of pairs of Nucléotide S by Génome and the degree of complexity of an organization. Thus, some Plant S and organizations Amphibien S have a Génome more than cash 100 billion pairs Nucléotide S is 30 times more than a Human genome. Indeed, the Génome of the cell S Eucaryote S seems to contain a broad excess of DNA. At the Mammalian S, less than 10% of the Génome would be useful for the expression in Protéine S or for the regulation of this expression.

The size of the Gène S can vary few hundreds with several tens of thousands of Nucléotide S. Cependant even longest Gène S do not use that a weak portion of their sequence to code the necessary information with the expression in Protéine S. These coding areas are called Exon S and the sequences not coding Intron S. Generally, plus the organization is complex, plus the quantity and the size of the Intron S is important. Thus the presence of will introns on the DNA from organizations Procaryote S is extremely rare. Certain areas of DNA are implied in the Régulation of the form of the genes. These sequences of regulation are generally upstream (side 5 ') or downstream localized (side 3 ') of a gene and more rarely inside Intron S or of Exon S.

Vitamins

See also: Vitamin

The Vitamin be (of Latin vita , life) They are organic compounds essential with the Vie, acting with very small quantities, for the development, the maintenance and the operation of the organization. Our cells are unable to synthesize them. With the risk of Vitamin deficiency, they must be brought by the food in the good proportions. The vitamin B1 (Thiamin), is the first vitamin which was discovered by Japanese Suzuki Umetaro seeking to look after the Béribéri (a disease due to the deficit in vitamin B1, characterized by muscular and neurological attacks). It was insulated by Kazimierz Funk (American biochemist of Polish origin) in 1912. Today, 13 different Vitamine S are known. It is a heterogeneous whole from the chemical and physiological point of view (mode of action). One classifies the Vitamine S in 2 units: the vitamins Water-soluble S (groups B and C) and the vitamins Liposoluble S (the groups has, D, E, and K). The water-soluble vitamins, are easily eliminated by the Rein S and sweat, the food must provide them daily. On the other hand, the liposoluble vitamins are stored in the fat Tissu and the Foie (from where the risk of overdose, especially for the vitamin has and D). Certain vitamins are cofactor S necessary to the activity of Enzyme S (vitamins of the group B), others constitute a reserve of being able reducing (Vitamine C, E). The functions of the majority of enter they remain to elucidate.

Under-disciplines of biochemistry

  • structural Biochemistry

  • metabolic Biochemistry
  • genetic Biochemistry
  • functional Biochemistry
  • medical Biochemistry and private clinic

Biochemistry, a multidisciplinary science

To conclude their studies, the biochemists call upon techniques and knowledge resulting from many scientific disciplines others that the Biologie, for example:

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