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Starting materials: the chemical elements of life[edit]



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Starting materials: the chemical elements of life[edit]


The main elements that compose the human body are shown from most abundant (by mass) to least abundant.



Main articles: Composition of the human body and Dietary mineral

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—carbonhydrogennitrogenoxygencalcium, 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.[32]

Biomolecules[edit]


The four main classes of molecules in biochemistry (often called biomolecules) are carbohydrateslipidsproteins, and nucleic acids.[33] Many biological molecules are polymers: in this terminology, monomers are relatively small micromolecules that are linked together to create largemacromolecules known as polymers. When monomers are linked together to synthesize a biological polymer, they undergo a process calleddehydration synthesis. Different macromolecules can assemble in larger complexes, often needed for biological activity.

Carbohydrates


Main articles: CarbohydrateMonosaccharideDisaccharide, and Polysaccharide

Carbohydrates

Glucose, a monosaccharide



A molecule of sucrose (glucose +fructose), a disaccharide





Amylose, a polysaccharide made up of several thousand glucose units

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 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,[34][a] and deoxyribose (C5H10O4).

A monosaccharide can switch from the acyclic (open-chain) form to a cyclic form, through a nucleophilic addition reaction between thecarbonyl group and one of the hydroxyls of the same molecule. The reaction creates a ring of carbon atoms closed by one bridgingoxygen atom. The resulting molecule has an hemiacetal or hemiketal group, depending on whether the linear form was an aldose or a ketose. The reaction is easily reversed, yielding the original open-chain form.[35]



Conversion between the furanoseacyclic, 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 withfuran 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 (the same of oxepane), rarely encountered, are called heptoses.

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.[36] Many monosaccharides joined together make a polysaccharide. They can be joined together in one long linear chain, or they may bebranched. 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


Main articles: LipidGlycerol, and Fatty acid

Structures of some common lipids. At the top are cholesterol and oleic acid.[37]The middle structure is a triglyceride composed of oleoylstearoyl, and palmitoylchains attached to a glycerol backbone. At the bottom is the commonphospholipidphosphatidylcholine.[38]



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 waxesfatty acids, fatty-acid derived phospho lipidssphingolipidsglycolipids, 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.[39]

Lipids are usually made from one molecule of glycerol combined with other molecules. Intriglycerides, 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).[40]

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.[41]

Lipids are an integral part of our daily diet. Most oils and milk products that we use for cooking and eating like buttercheeseghee etc., are composed of fatsVegetable oils are rich in variouspolyunsaturated 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 ortransfersome).


Proteins


Main articles: Protein and Amino acid

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



Generic amino acids (1) in neutral form, (2) as they exist physiologically, and (3) joined together as a dipeptide.



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 —COOunder 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.[42]

A schematic ofhemoglobin. The red and blue ribbons represent the protein globin; the green structures are the hemegroups.

Some proteins perform largely structural roles. For instance, movements of the proteins actin and myosinultimately 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. 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 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 anα-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.[43]



Examples of protein structures from the Protein Data Bank




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 isoleucineleucinelysinemethioninephenylalaninethreoninetryptophan, and valine. These are the essential amino acids, since it is essential to ingest them. Mammals do possess the enzymes to synthesize alanineasparagineaspartatecysteineglutamateglutamineglycineprolineserine, andtyrosine, 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.[44]

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. Unicellularorganisms, 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.[45]

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.[46] 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


Main articles: Nucleic acidDNARNA, and Nucleotides


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

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.[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.[47]

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

The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).[48] 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 adeninecytosine,guaninethymine, 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.[49] 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.



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