Free download. Book file PDF easily for everyone and every device. You can download and read online Theoretical Biochemistry - Processes and Properties of Biological Systems, Volume 9 file PDF Book only if you are registered here. And also you can download or read online all Book PDF file that related with Theoretical Biochemistry - Processes and Properties of Biological Systems, Volume 9 book. Happy reading Theoretical Biochemistry - Processes and Properties of Biological Systems, Volume 9 Bookeveryone. Download file Free Book PDF Theoretical Biochemistry - Processes and Properties of Biological Systems, Volume 9 at Complete PDF Library. This Book have some digital formats such us :paperbook, ebook, kindle, epub, fb2 and another formats. Here is The CompletePDF Book Library. It's free to register here to get Book file PDF Theoretical Biochemistry - Processes and Properties of Biological Systems, Volume 9 Pocket Guide.

High fat oxidation was responsible for the insulin resistance. 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 of the gene. Watson , Francis Crick , Rosalind Franklin , and Maurice Wilkins were instrumental in solving DNA structure and suggesting its relationship with genetic transfer of information.

Fire and Craig C. 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.

In addition to the six major elements that compose most of the human body, humans require smaller amounts of possibly 18 more. The four main classes of molecules in biochemistry often called biomolecules are carbohydrates , lipids , proteins , and nucleic acids. 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.

Two of the main functions of carbohydrates are energy storage and providing structure. Sugars are carbohydrates, but not all carbohydrates are sugars.

  • Design engineering manual.
  • The Shepherd of Weeds (The Poisons of Caux, Book 3)?
  • Stanford Libraries!
  • Biochemistry - Wikipedia.
  • Hematopoietic Differentiation of Human Pluripotent Stem Cells?

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 generalized formula C n H 2 n O n , where n is at least 3. Glucose C 6 H 12 O 6 is one of the most important carbohydrates; others include fructose C 6 H 12 O 6 , the sugar commonly associated with the sweet taste of fruits , [35] [a] and deoxyribose C 5 H 10 O 4 , a component of DNA.

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. 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 carbon-carbon 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. 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.

Biomolecules (Updated)

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 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.

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. 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. Most lipids have some polar character in addition to being largely nonpolar. In general, the bulk of their structure is nonpolar or hydrophobic "water-fearing" , meaning that it does not interact well with polar solvents like water.

Another part of their structure is polar or hydrophilic "water-loving" and will tend to associate with polar solvents like water. This makes them amphiphilic molecules having both hydrophobic and hydrophilic portions. In the case of cholesterol , the polar group is a mere —OH hydroxyl or alcohol. In the case of phospholipids, the polar groups are considerably larger and more polar, as described below. Lipids are an integral part of our daily diet.

Most oils and milk products that we use for cooking and eating like butter , cheese , ghee etc. 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.

Proteins are very large molecules—macro-biopolymers—made from monomers called amino acids. 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 amino acid residues. 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.

Enzymes: principles and biotechnological applications

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. 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 10 11 or more; a reaction that would normally take over 3, years to complete spontaneously might take less than a second with an enzyme.

Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, CAS

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.

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 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. 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. The amino acids may then be linked together to make a protein. A similar process is used to break down proteins. It is first hydrolyzed into its component amino acids. 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. 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. By finding how similar two protein sequences are, we acquire knowledge about their structure and therefore their function.

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. 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.

Glucose is an energy source in most life forms. For instance, polysaccharides are broken down into their monomers by enzymes glycogen phosphorylase removes glucose residues from glycogen, a polysaccharide. Disaccharides like lactose or sucrose are cleaved into their two component monosaccharides. Glucose is mainly metabolized by a very important ten-step pathway called glycolysis , the net result of which is to break down one molecule of glucose into two molecules of pyruvate. This 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.

Other monosaccharides like galactose and fructose can be converted into intermediates of the glycolytic pathway. 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 FADH 2 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. This is why humans breathe in oxygen and breathe out carbon dioxide.

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. 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 is not a defined line between these disciplines. Biochemistry studies the chemistry required for biological activity of molecules, molecular biology studies their biological activity, genetics studies their heredity, which happens to be carried by their genome. This is shown in the following schematic that depicts one possible view of the relationships between the fields: [55].

Extremophiles are microorganisms which live in extreme conditions, some of which may provide some exceptions or variations on some of the natural laws cited above. For example, in July , a scientific study of Kidd Mine in Canada discovered sulfur-breathing organisms which live feet below the surface, and which breathe sulfur in order to survive. Glucose and sucrose are also found in varying quantities in various fruits, and sometimes exceed the fructose present.

However, peaches contain more sucrose 6. From Wikipedia, the free encyclopedia. For the journals, see Biochemistry journal and Biological Chemistry journal. Index Outline. Main article: History of biochemistry. Main articles: Composition of the human body and Dietary mineral. Main article: Biomolecule. Main articles: Carbohydrate , Monosaccharide , Disaccharide , and Polysaccharide.

  • Math Study Skills Workbook (4th Edition).
  • Theoretical Biochemistry, Volume 9 - 1st Edition.
  • History of biochemistry?

Glucose, a monosaccharide. Comparison of the models for Bdependent carbon-skeleton mutases. The partial-proton-transfer concept. Carloni and U.


Principles of the Car-Parinello method. Car-Parinello modelling of biological systems. Applications to non-enzymatic systems. Applications to enzymes. Kolmodin, V. Luzhkov and J. Protein tyrosine phosphatase reactions. The empirical valence bond method. Substrate trapping in cysteine to serine mutated PTPases. Prediction of a ligand induced conformational change in the active site of CDC25A. Kinetic isotope effects in phosphoryl transfer reactions.

Verkhivker, D. Bouzida, D. Gehlhaar, P. Rejto, L. Schaffer, S. Arthurs, A. Colson, S. Freer, V. Larson, B. A: Luty, T. Marrone and P. Structural models for molecular recognition. Structure-based analysis of HIV-1 protease-inhibitor binding. Structure-based computational models of ligand-protein binding dynamics and molecular docking. Computer simulations of ligand-protein binding. Computer simulations of HIV-1 protease-inhibitor binding dynamics and thermodynamics.

Higgs and C. Receptor structure and modelling. Ligand binding. Structural changes. Receptor-G-protein interactions. GPCR dimerisation. Pastor and H. TBP and transcription. TATA box sequence specific recognition. Dynamics effects in complex stabilization. Towards the preinitiation complex assembly. Wetmore, L. Eriksson and R. Characterization of DNA radiation products. Full DNA studies. Multi-component model for DNA radiation damage.

Adamo, M. Cossi, N. Rega and V. The density functional model. Vibrational averaging. Solvent effects. Modelling Enzyme-Ligand Interactions M. Ramos, A. Melo and E. Strategies in enzyme-ligand design. The enzyme-ligand complex in motion. A quantum insight into the study of enzyme-ligand interactions.

Techniques for reaction modelling. Practical aspects of modelling enzyme reactions. Some recent applications. Quinones and Quinoidal Radicals in Photosynthesis R. Tests of computational methods for calculating properties of quinoidal radicals. Calculated properties of quinoidal radicals important in photosynthesis. Semiquinone radical anions in plant photosystem II.