HUMAN HEALTH AND DISEASE

BIOLOGY INVESTIGATORY PROJECT:-

PREPARED BY –

MASTER ADITYA SWARNAKAR

ROLL NO. ……….., CLASS-XII

KENDRIYA VIDYALAYA, SECTOR-6,

ROURKELA

GUIDED BY – Ms, SANDHYA KHALKO,

LABORATORY CERTIFICATE

Certified that this is the bonafide record of the work done by Master AdityaSwarnakar bearing Roll No…………… of class XII in the academic

session 2015-16 in the Biology laboratory of Kendriya Vidyalaya, Sector-6, Rourkela.

The Project has been done in the intellectual and inspiring

environment of Ms.Sandhya Khalko.

Signature of Student

Signature of External Signature of Internal

ACKNOWLEDGEMENT

I am thankful to Kendriya Vidyalaya, Sector-6, Rourkela for giving me an opportunity to prove my skills. In the process of preparing the project I have made use of theoretical knowledge that I have gained in my class.

I owe my sincere thanks to my Biology teacher Ms.Sandhya Khalko without whose intervention this project would not have been the same. Her constant motivation and positive complement have added to the successive completion of the project.

Lastly, I express my sincere thanks to my family and friends who have extended helping hands in completing the project.

Signature of Student

Signature of Teacher Signature of External

KENDRIYA VIDYALAYASECTOR-6, ROURKELAPHYSICS INVESTIGATORY PROJECT2015-16

AIM – TO DETERMINE THE REFRACTIVE INDEX OF VARIOUS LIQUID USING RECTAGULAR HOLLOW GLASS SLAB.

LABORATRY CERTIFICATE

This is to certify that Aditya Swarnakar a student of class XII has successfully completed the research project on the topic “to determine the refractive index of various

liquid using rectangular hollow glass slab” under the guidance of Mr. L. M. Sahu (subject teacher).The references taken in making this project have been declared at the end of the report.

Signature of Examiner Signature of lab in –charge

Signature of Principal

DECLARATION

I Aditya Swarnakar of class XII has successfully completed the research project on the topic “to determine the refractive index of various liquid using rectangular hollow glass slab” is done by me under the guidance of our teacher Mr. L. M. Sahu.

Name- Aditya SwarnakarClass-XIIRoll No.-

ACKNOWLEDGEMENTI wish my gratitude and sincere thanks to our principal for his encouragement

and for all the facilities that he provided for this project work. I sincerely appreciate his magnanimity by taking of into his folds for which I shall remain indebted to him. I extend my hereby thanks to Mr. L. M. Sahu our Physics teacher, who guided me to the successful completion of this project.

I cannot forge to offer my sincere thanks to my friends who helped me to carry out the project successfully and for the valuable advice and support, which I received from them time to time.

Name- Aditya SwarnakarClass-XIIRoll No.-

BiomoleculeFrom Wikipedia, the free encyclopedia

A representation of the 3D structure of myoglobin, showingalpha helices, represented by ribbons. This protein

was the first to have its structure solved by X-ray crystallography by Max Perutz andSir John Cowdery

Kendrew in 1958, for which they received a Nobel Prize in Chemistry

A biomolecule is any molecule that is present in living organisms, including largemacromolecules such as proteins, carbohydrates, lipids, and nucleic acids, as well assmall 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.

Contents

Biomolecular engineering is the application of engineering principles and practices to the purposeful manipulation of molecules of biological origin. Biomolecular engineers integrate knowledge of biological processes with the core knowledge of chemical engineering in order to focus on molecular level solutions to issues and problems in the life sciences related to the environment, agriculture, energy, industry, food production, biotechnology and medicine. Biomolecular engineers purposefully manipulate carbohydrates, proteins, nucleic acids and lipids within the framework of the relation between their structure (see: nucleic acid structure, carbohydrate chemistry, protein structure,), function (see: protein function) and properties and in relation to applicability to such areas as environmental remediation, crop and live stock production, biofuel cells and biomolecular diagnostics. Fundamental attention is given to the thermodynamics and kinetics of molecular recognition in enzymes, antibodies, DNA hybridization, bio-conjugation/bio-immobilization and bioseparations. Attention is also given to the rudiments of engineered biomolecules in cell signaling, cell growth kinetics, biochemical pathway engineering and bioreactor engineering. Biomolecular engineers are leading the major shift towards understanding and controlling the molecular mechanisms that define life as we know it.

Contents  [hide] 

1Timelineo 1.1Historyo 1.2Future

2Basic biomolecules

o 2.1Proteinso 2.2Carbohydrateso 2.3Nucleic acidso 2.4Lipids

3Biomolecular engineering of moleculeso 3.1Recombinant DNA

3.1.1Method 3.1.2Applications

o 3.2Site-directed mutagenesis 3.2.1General procedure 3.2.2Applications

o 3.3Bio-immobilization and bio-conjugationo 3.4Polymerase chain reaction

3.4.1Biomolecular engineering techniques involved in PCRo 3.5Enzyme-linked immunosorbent assay (ELISA)

3.5.1Biomolecular engineering techniques involved in ELISA 4Applications and fields

o 4.1Biomolecular engineering in industry 4.1.1Scale-up

o 4.2Related industries 4.2.1Bioengineering 4.2.2Biochemistry 4.2.3Biochemical engineering 4.2.4Biotechnology 4.2.5Bioelectrical engineering 4.2.6Biomedical engineering

o 4.3Chemical engineeringo 4.4Education and programs

5See also 6References 7Further reading 8External links

Timeline[edit]History[edit]During World War II,[1] the need for large quantities of penicillin of acceptable quality brought together chemical engineers and microbiologists to focus on penicillin production. This created the right conditions to start a chain of reactions that lead to the creation of the field of biomolecular engineering. Biomolecular engineering was first defined in 1992 by the National Institutes of Health as research at the interface of chemical engineering and biology with an emphasis at the molecular level". Although first defined as research, biomolecular engineering has since become an academic discipline and a field of engineering practice. Herceptin, a humanized Mab for breast cancer treatment, became the first drug designed by a biomolecular engineering approach and was approved by the FDA. Also, Biomolecular Engineering was a former name of the journal New Biotechnology.

Future[edit]

Bio-inspired technologies of the future can help explain biomolecular engineering. Looking at the Moore's law "Prediction", in the future quantum and biology-based processors are "big" technologies. With the use of biomolecular engineering, the way our processors work can be manipulated in order to function in the same sense a biological cell work. Biomolecular engineering has the potential to become one of the most important scientific disciplines because of its advancements in the analyses of gene expression patterns as well as the purposeful manipulation of many important biomolecules to improve functionality. Research in this field may lead to new drug discoveries, improved therapies, and advancement in new bioprocess technology. With the increasing knowledge of biomolecules, the rate of finding new high-value molecules including but not limited to antibodies, enzymes, vaccines, and therapeutic peptides will continue to accelerate. Biomolecular engineering will produce new designs for therapeutic drugs and high-value biomolecules for treatment or prevention of cancers, genetic diseases, and other types of metabolic diseases. Also, there is anticipation of industrial enzymes that are engineered to have desirable properties for process improvement as well the manufacturing of high-value biomolecular products at a much lower production cost. Using recombinant technology, new antibiotics that are active against resistant strains will also be produced.[2]

Basic biomolecules[edit]Biomolecular engineering deals with the manipulation of many key biomolecules. These include, but are not limited to, proteins, carbohydrates, nucleic acids, and lipids. These molecules are the basic building blocks of life and by controlling, creating, and manipulating their form and function there are many new avenues and advantages available to society. Since every biomolecule is different, there are a number of techniques used to manipulate each one respectively.

Proteins[edit]Proteins are polymers that are made up of amino acid chains linked with peptide bonds. They have four distinct levels of structure: primary, secondary, tertiary, and quaternary. Primary structure refers to the amino acid backbone sequence. Secondary structure focuses on minor conformations that develop as a result of the hydrogen bonding between the amino acid chain. If most of the protein contains intermolecular hydrogen bonds it is said to be fibrillar, and the majority of its secondary structure will be beta sheets. However, if the majority of the orientation contains intramolecular hydrogen bonds, then the protein is referred to as globular and mostly consists of alpha helixes. There are also conformations that consist of a mix of alpha helices and beta sheets as well as a beta helixes with an alpha sheets.

The tertiary structure of proteins deal with their folding process and how the overall molecule is arranged. Finally, a quaternary structure is a group of tertiary proteins coming together and binding. With all of these levels, proteins have a wide variety of places in which they can be manipulated and adjusted. Techniques are used to affect the amino acid sequence of the protein (site directed mutagenesis), the folding and conformation of the protein, or the folding of a single tertiary protein within a quaternary protein matrix. Proteins that are the main focus of manipulation are typically enzymes. These are proteins that act as catalysts for biochemical reactions. By manipulating these catalysts, the reaction rates, products, and effects can be controlled. Enzymes and proteins are important to the biological field and research that there are specific subsets of engineering focusing only on proteins and enzymes. See protein engineering.

Carbohydrates[edit]Carbohydrates are another important biomolecule. These are polymers, called polysaccharides, which are made up of chains of simple sugars connected via glycosidic bonds. These monosaccharides consist of a five to six carbon ring that contains carbon, hydrogen, and oxygen - typically in a 1:2:1 ratio, respectively. Common monosaccharides are glucose,fructose, and ribose. When linked together monosaccharides can form disaccharides, oligosaccharides, and

polysaccharides: the nomenclature is dependent on the number of monosaccharides linked together. Common dissacharides, two monosaccharides joined together, are sucrose, maltose, and lactose. Important polysaccharides, links of many monosaccharides, are cellulose, starch, and chitin.

Cellulose is a polysaccharide made up of beta 1-4 linkages between repeat glucose monomers. It is the most abundant source of sugar in nature and is a major part of the paper industry. Starch is also a polysaccharide made up of glucose monomers; however, they are connected via an alpha 1-4 linkage instead of beta. Starches, particularly amylase, are important in many industries, including the paper, cosmetic, and food. Chitin is a derivation of cellulose, possessing anacetamide group instead of an –OH on one of its carbons. Acetimide group is deacetylated the polymer chain is then calledchitosan. Both of these cellulose derivatives are a major source of research for the biomedical and food industries. They have been shown to assist with blood clotting, have antimicrobial properties, and dietary applications. A lot of engineering and research is focusing on the degree of deacetylation that provides the most effective result for specific applications.

Nucleic acids[edit]Nucleic acids are macromolecules that consist of DNA and RNA which are biopolymers consisting of chains of biomolecules. These two molecules are the genetic code and template that make life possible. Manipulation of these molecules and structures causes major changes in function and expression of other macromolecules. Nucleosides are glycosylamines containing a nucleobase bound to either ribose or deoxyribose sugar via a beta-glycosidic linkage. The sequence of the bases determine the genetic code. Nucleotides are nucleosides that are phosphorylated by specific kinases via aphosphodiester bond.[3] Nucleotides are the repeating structural units of nucleic acids. The nucleotides are made of a nitrogenous base, a pentose (ribose for RNA or deoxyribose for DNA), and three phosphate groups. See, Site-directed mutagenesis, recombinant DNA, and ELISAs.

Lipids[edit]Lipids are biomolecules that are made up of glycerol derivatives bonded with fatty acid chains. Glycerol is a simple polyolthat has a formula of C3H5(OH)3. Fatty acids are long carbon chains that have a carboxylic acid group at the end. Thecarbon chains can be either saturated with hydrogen; every carbon bond is occupied by a hydrogen atom or a single bond to another carbon in the carbon chain, or they can be unsaturated; namely, there are double bonds between the carbon atoms in the chain. Common fatty acids include lauric acid, stearic acid, and oleic acid. The study and engineering of lipids typically focuses on the manipulation of lipid membranes and encapsulation. Cellular membranes and other biological membranes typically consist of a phospholipid bilayer membrane, or a derivative thereof. Along with the study of cellular membranes, lipids are also important molecules for energy storage. By utilizing encapsulation properties and thermodynamiccharacteristics, lipids become significant assets in structure and energy control when engineering molecules.

Biomolecular engineering of molecules[edit]Recombinant DNA[edit]Main article: Recombinant DNA

Recombinant DNA are DNA biomolecules that contain genetic sequences that are not native to the organism’s genome. Using recombinant techniques, it is possible to insert, delete, or alter a DNA sequence precisely without depending on the location of restriction sites. There are a wide range of applications for which recombinant DNA is used.

Method[edit]

Creating recombinant DNA. After the plasmid is cleaved by restriction enzymes, ligases insert the foreign DNA

fragments into the plasmid.

The traditional method for creating recombinant DNA typically involves the use ofplasmids in the host bacteria. The plasmid contains a genetic sequence corresponding to the recognition site of a restriction endonuclease, such as EcoR1. After foreign DNA fragments, which have also been cut with the same restriction endonuclease, have been inserted into host cell, the restriction endonuclease gene is expressed by applying heat,[4] or by introducing a biomolecule, such as arabinose.[5] Upon expression, the enzyme will cleave the plasmid at its corresponding recognition site creating sticky ends on the plasmid. Ligases then joins the sticky ends to the corresponding sticky ends of the foreign DNA fragments creating a recombinant DNA plasmid.

Advances in genetic engineering have made the modification of genes in microbes quite efficient allowing constructs to be made in about a weeks worth of time. It has also made it possible to modify the organism's genome itself. Specifically, use of the genes from the bacteriophage lambda are used in recombination.[6] This mechanism, known as recombineering, utilizes the three proteins Exo, Beta, and Gam, which are created by the genes exo, bet, and gam respectively. Exo is a double stranded DNA exonuclease with 5’ to 3’ activity. It cuts the double stranded DNA leaving 3’ overhangs. Beta is a protein that binds to single stranded DNA and assists homologous recombination by promoting annealing between the homology regions of the inserted DNA and the chromosomal DNA. Gam functions to protect the DNA insert from being destroyed by nativenucleases within the cell.

Applications[edit]Recombinant DNA can be engineered for a wide variety of purposes. The techniques utilized allow for specific modification of genes making it possible to modify any biomolecule. It can be engineered for laboratory purposes, where it can be used to analyze genes in a given organism. In the pharmaceutical industry, proteins can be modified using recombination techniques. Some of these proteins include human insulin. Recombinant insulin is synthesized by inserting the human insulin gene into E. coli, which then produces insulin for human use.[7][8] Other proteins, such as human growth hormone,[9] factor VIII, and hepatitis B vaccine are produced using similar means. Recombinant DNA can also be used for diagnostic methods involving the use of the ELISA method. This makes it possible to engineer antigens, as well as the enzymes attached, to recognize different substrates or be modified for bioimmobilization. Recombinant DNA is also responsible for many products found in the agricultural industry. Genetically modified food, such as golden rice,[10] has been engineered to have increased production of vitamin A for use in societies and cultures where dietary vitamin A is scarce. Other properties that have been engineered into crops include herbicide-resistance[11] and insect-resistance.[12]

Site-directed mutagenesis[edit]Site-directed mutagenesis is a technique that has been around since the 1970s. The early days of research in this field yielded discoveries about the potential of certain chemicals such as bisulfite

and aminopurine to change certain bases in a gene. This research continued, and other processes were developed to create certain nucleotide sequences on a gene, such as the use of restriction enzymes to fragment certain viral strands and use them as primers for bacterial plasmids. The modern method, developed by Michael Smith in 1978, uses an oligonucleotide that is complementary to a bacterial plasmid with a single base pair mismatch or a series of mismatches. [13]

General procedure[edit]Site directed mutagenesis is a valuable technique that allows for the replacement of a single base in an oligonucleotide or gene. The basics of this technique involve the preparation of a primer that will be a complementary strand to a wild type bacterial plasmid. This primer will have a base pair mismatch at the site where the replacement is desired. The primer must also be long enough such that the primer will anneal to the wild type plasmid. After the primer anneals, a DNA polymerase will complete the primer. When the bacterial plasmid is replicated, the mutated strand will be replicated as well. The same technique can be used to create a gene insertion or deletion. Often, an antibiotic resistant gene is inserted along with the modification of interest and the bacteria are cultured on an antibiotic medium. The bacteria that were not successfully mutated will not survive on this medium, and the mutated bacteria can easily be cultured.

This animation shows the basic steps of site directed mutagenesis, where X-Y is the desired base pair

replacement of T-A.

Applications[edit]Site-directed mutagenesis can be useful for many different reasons. A single base pair replacement, could change a codon, and thus replace an amino acid in a protein. This is useful for studying the way certain proteins behave. It is also useful because enzymes can be purposefully manipulated by changing certain amino acids. If an amino acid is changed that is in close proximity to the active site, the kinetic parameters may change drastically, or the enzyme might behave in a different way. Another application of site directed mutagenesis is exchanging an amino acid residue far from the active site with a lysine residue or cysteine residue. These amino acids make it easier to covalently bond the enzyme to a solid surface, which allows for enzyme re-use and use of enzymes in continuous processes. Sometimes, amino acids with non-natural functional groups (such as ketones and azides) are added to proteins[14] These additions may be for ease of bioconjugation, or to study the effects of amino acid changes on the form and function of the proteins. The coupling of site directed mutagenesis and PCR are being utilized to reduce interleukin-6 activity in cancerous cells.[15] The bacteria bacillus subtilis is often used in site directed mutagenesis.[16] The bacteria secretes an enzyme called subtilisin through the cell wall. Biomolecular engineers can purposely manipulate this gene to essentially make the cell a factory for producing whatever protein the insertion in the gene codes.

Bio-immobilization and bio-conjugation[edit]

Bio-immobilization and bio-conjugation is the purposeful manipulation of a biomolecule’s mobility by chemical or physical means to obtain a desired property. Immobilization of biomolecules allows exploiting characteristics of the molecule under controlled environments. For example [17] , the immobilization of glucose oxidase on calcium alginate gel beads can be used in a bioreactor. The resulting product will not need purification to remove the enzyme because it will remain linked to the beads in the column. Examples of types of biomolecules that are immobilized are enzymes, organelles, and complete cells. Biomolecules can be immobilized using a range of techniques. The most popular are physical entrapment, adsorption, and covalent modification.

Physical entrapment[18] - the use of a polymer to contain the biomolecule in a matrix without chemical modification. Entrapment can be between lattices of polymer, known as gel entrapment, or within micro-cavities of synthetic fibers, known as fiber entrapment. Examples include entrapment of enzymes such as glucose oxidase in gel column for use as abioreactor. Important characteristic with entrapment is biocatalyst remains structurally unchanged, but creates large diffusion barriers for substrates.

Adsorption - immobilization of biomolecules due to interaction between the biomolecule and groups on support. Can be physical adsorption, ionic bonding, or metal binding chelation. Such techniques can be performed under mild conditions and relatively simple, although the linkages are highly dependent upon pH, solvent and temperature. Examples include enzyme-linked immunosorbent assays.

Covalent modification- involves chemical reactions between certain functional groups and matrix. This method forms stable complex between biomolecule and matrix and is suited for mass production. Due to the formation of chemical bond to functional groups, loss of activity can occur. Examples of chemistries used are DCC coupling[19] PDC coupling and EDC/NHS coupling, all of which take advantage of the reactive amines on the biomolecule’s surface.

Because immobilization restricts the biomolecule, care must be given to ensure that functionality is not entirely lost. Variables to consider are pH,[20] temperature, solvent choice, ionic strength, orientation of active sites due to conjugation. For enzymes, the conjugation will lower the kinetic rate due to a change in the 3-dimensional structure, so care must be taken to ensure functionality is not lost. Bio-immobilization is used in technologies such as diagnostic bioassays, biosensors,ELISA, and bioseparations. Interleukin (IL-6) can also be bioimmobilized on biosensors. The ability to observe these changes in IL-6 levels is important in diagnosing an illness. A cancer patient will have elevated IL-6 level and monitoring those levels will allow the physician to watch the disease progress. A direct immobilization of IL-6 on the surface of a biosensor offers a fast alternative to ELISA.[21]

Polymerase chain reaction[edit]Main article: Polymerase chain reaction

Polymerase chain reaction. There are three main steps involved in PCR. In the first step, the double stranded

DNA strands are "melted" or denatured forming single stranded DNA. Next, primers, which have been

designed to target a specific gene sequence on the DNA, anneal to the single stranded DNA. Lastly, DNA

polymerase synthesizes a new DNA strand complimentary to the original DNA. These three steps are repeated

multiple times until the desired number of copies are made.

The polymerase chain reaction (PCR) is a scientific technique that is used to replicate a piece of a DNA molecule by several orders of magnitude. PCR implements a cycle of repeated heated and cooling known as thermal cycling along with the addition of DNA primers and DNA polymerases to selectively replicate the DNA fragment of interest. The technique was developed by Kary Mullis in 1983 while working for the Cetus Corporation.Mullis would go on to win the Nobel Prize in Chemistry in 1993 as a result of the impact thatPCR had in many areas such as DNA cloning, DNA sequencing, and gene analysis.[22]

Biomolecular engineering techniques involved in PCR[edit]A number of biomolecular engineering strategies have played a very important role in the development and practice of PCR. For instance a crucial step in insuring the accurate replication of the desired DNA fragment is the creation of the correct DNA primer. The most common method of primer synthesis is by the phosphoramidite method. This method includes the biomolecular engineering of a number of molecules to attain the desired primer sequence. The most prominent biomolecular engineering technique seen in this primerdesign method is the initial bioimmobilization of a nucleotide to a solid support. This step is commonly done via the formation of a covalent bond between the 3’-hydroxy group of the first nucleotide of the primer and the solid support material. [23]

Furthermore, as the DNA primer is created certain functional groups of nucleotides to be added to the growing primer require blocking to prevent undesired side reactions. This blocking of functional groups as well as the subsequent de-blocking of the groups, coupling of subsequent nucleotides, and eventual cleaving from the solid support[23] are all methods of manipulation of biomolecules that

can be attributed to biomolecular engineering. The increase in interleukin levels is directly proportional to the increased death rate in breast cancer patients. PCR paired with Western blotting and ELISA help define the relationship between cancer cells and IL-6. [24]

Enzyme-linked immunosorbent assay (ELISA)[edit]Main article: ELISA

Enzyme-linked immunosorbent assay is an assay that utilizes the principle of antibody-antigen recognition to test for the presence of certain substances. The three main types ofELISA tests which are indirect ELISA, sandwich ELISA, and competitive ELISA all rely on the fact that antibodies have an affinity for only one specific antigen. Furthermore, theseantigens or antibodies can be attached to enzymes which can react to create a colorimetric result indicating the presence of the antibody or antigen of interest.[25] Enzyme linked immunosorbent assays are used most commonly as diagnostic tests to detect HIV antibodies in blood samples to test for HIV, human chorionic gonadotropin molecules in urine to indicate pregnancy, and Mycobacterium tuberculosis antibodies in blood to test patients for tuberculosis. Furthermore, ELISA is also widely used as a toxicology screen to test people's serum for the presence of illegal drugs.

Biomolecular engineering techniques involved in ELISA[edit]Although there are three different types of solid state enzyme-linked immunosorbent assays, all three types begin with the bioimmobilization of either an antibody or antigen to a surface. This bioimmobilization is the first instance of biomolecular engineering that can be seen in ELISA implementation. This step can be performed in a number of ways including a covalent linkage to a surface which may be coated with protein or another substance. The bioimmobilization can also be performed via hydrophobic interactions between the molecule and the surface. Because there are many different types of ELISAs used for many different purposes the biomolecular engineering that this step requires varies depending on the specific purpose of the ELISA.

Another biomolecular engineering technique that is used in ELISA development is the bioconjugation of an enzyme to either an antibody or antigen depending on the type of ELISA. There is much to consider in this enzyme bioconjugation such as avoiding interference with the active site of the enzyme as well as the antibody binding site in the case that the antibody is conjugated with enzyme. This bioconjugation is commonly performed by creating crosslinks between the two molecules of interest and can require a wide variety of different reagents depending on the nature of the specific molecules.[26]

Interleukin (IL-6) is a signaling protein that has been known to be present during an immune response. The use of the sandwich type ELISA quantifies the presence of this cytokine within spinal fluid or bone marrow samples.[27]

Applications and fields[edit]Biomolecular engineering in industry[edit]

Graph showing number of biotech companies per country[28]

Graph showing percentages of biotech firms by application [29]

Biomolecular engineering is an extensive discipline with applications in many different industries and fields. As such, it is difficult to pinpoint a general perspective on the Biomolecular engineering profession. The biotechnology industry, however, provides an adequate representation. The biotechnology industry, or biotech industry, encompasses all firms that use biotechnology to produce goods or services or to perform biotechnology research and development. [28] In this way, it encompasses many of the industrial applications of the biomolecular engineering discipline. By examination of the biotech industry, it can be gathered that the principal leader of the industry is the United States, followed by France and Spain.[28] It is also true that the focus of the biotechnology industry and the application of biomolecular engineering is primarily clinical and medical. People are willing to pay for good health, so most of the money directed towards the biotech industry stays in health-related ventures.[citation needed]

Scale-up[edit]Scaling up a process involves using data from an experimental-scale operation (model or pilot plant) for the design of a large (scaled-up) unit, of commercial size. Scaling up is a crucial part of commercializing a process. For example, insulinproduced by genetically modified Escherichia coli bacteria was initialized on a lab-scale, but to be made commercially viable had to be scaled up to an industrial level. In order to achieve this scale-up a lot of lab data had to be used to design commercial sized units. For example, one of the steps in insulin production involves the crystallization of high purity glargin insulin.[30] In order to achieve this process on a large scale we want to keep the Power/Volume ratio of both the lab-scale and large-scale crystallizers the same in order to achieve homogeneous mixing.[31] We also assume the lab-scale crystallizer has geometric similarity to the large-scale crystallizer. Therefore,

P/V α Ni3di

3

where di= crystallizer impeller diameterNi= impeller rotation rate

Related industries[edit]Bioengineering[edit]Main article: Biological engineering

A broad term encompassing all engineering applied to the life sciences. This field of study utilizes the principles of biologyalong with engineering principles to create marketable products. Some bioengineering applications include:

Biomimetics  - The study and development of synthetic systems that mimic the form and function of natural biologically produced substances and processes.

Bioprocess engineering  - The study and development of process equipment and optimization that aids in the production of many products such as food and pharmaceuticals.

Industrial microbiology  - The implementation of microorganisms in the production of industrial products such as food andantibiotics. Another common application of industrial microbiology is the treatment of wastewater in chemical plants via utilization of certain microorganisms.

Biochemistry[edit]Main article: Biochemistry

Biochemistry is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemical processes govern all living organisms and living processes and the field of biochemistry seeks to understand and manipulate these processes.

Biochemical engineering[edit]Main article: Biochemical engineering

Biocatalysis  – Chemical transformations using enzymes. Bioseparations  – Separation of biologically active molecules. Thermodynamics  and Kinetics (chemistry) – Analysis of reactions

involving cell growth and biochemicals. Bioreactor  design and analysis – Design of reactors for performing

biochemical transformations.

Biotechnology[edit]Main article: Biotechnology

Biomaterials  – Design, synthesis and production of new materials to support cells and tissues.

Genetic engineering  – Purposeful manipulation of the genomes of organisms to produce new phenotypic traits.

Bioelectronics , Biosensor and Biochip – Engineered devices and systems to measure, monitor and control biological processes.

Bioprocess engineering  – Design and maintenance of cell-based and enzyme-based processes for the production of fine chemicals and pharmaceuticals.

Bioelectrical engineering[edit]

Main article: Bioelectric

Bioelectrical engineering involves the electrical fields generated by living cells or organisms. Examples include the electric potential developed between muscles or nerves of the body. This discipline requires knowledge in the fields of electricity andbiology to understand and utilize these concepts to improve or better current bioprocesses or technology.

Bioelectrochemistry  - Chemistry concerned with electron/proton transport throughout the cell

Bioelectronics  - Field of research coupling biology and electronics

Biomedical engineering[edit]Main article: Biomedical engineering

Biomedical engineering is a sub category of bioengineering that uses many of the same principles but focuses more on the medical applications of the various engineering developments. Some applications of biomedical engineering include:

Biomaterials  - Design of new materials for implantation in the human body and analysis of their effect on the body.

Cellular engineering  – Design of new cells using recombinant DNA and development of procedures to allow normal cells to adhere to artificial implanted biomaterials

Tissue engineering  – Design of new tissues from the basic biological building blocks to form new tissues

Artificial organs  – Application of tissue engineering to whole organs Medical imaging  – Imaging of tissues using CAT

scan, MRI, ultrasound, x-ray or other technologies Medical Optics and Lasers – Application of lasers to medical

diagnosis and treatment Rehabilitation engineering  – Design of devices and systems used to

aid the disabled Man-machine interfacing - Control of surgical robots and remote

diagnostic and therapeutic systems using eye tracking, voice recognition and muscle and brain wave controls

Human factors and ergonomics  – Design of systems to improve human performance in a wide range of applications

Chemical engineering[edit]Main article: Chemical engineering

Chemical engineering is the processing of raw materials into chemical products. It involves preparation of raw materials to produce reactants, the chemical reaction of these reactants under controlled conditions, the separation of products, the recycle of byproducts, and the disposal of wastes. Each step involves certain basic building blocks called “unit operations,” such as extraction, filtration, and distillation.[32] These unit operations are found in all chemical processes. Biomolecular engineering is a subset of Chemical Engineering that applies these same principles to the processing of chemical substances made by living organisms.

Education and programs[edit]This section needs additional citations for verification. Please help improve this article by adding citations to reliable sources. Unsourced material may be challenged and removed. (June 2014)

The discipline of biomolecular engineering has become ever more prevalent with the better understanding and advancement of current sciences and technologies. In previous years, biomolecular engineering was not a well-known career path, but the growth in popularity of this subject has resulted in new programs offered to undergraduate and graduate students. [citation needed]

Newly developed and offered undergraduate programs across the United States, often coupled to the chemical engineering program, allow students to achieve a B.S. degree. According to ABET (Accreditation Board for Engineering and Technology), biomolecular engineering curricula "must provide thorough grounding in the basic sciences including chemistry, physics, and biology, with some content at an advanced level… [and] engineering application of these basic sciences to design, analysis, and control, of chemical, physical, and/or biological processes."[33] Common curricula consist of major engineering courses including transport, thermodynamics, separations, and kinetics, with additions of life sciencescourses including biology and biochemistry, and including specialized biomolecular courses focusing on cell biology, nano- and biotechnology, biopolymers, etc.[34]

To further education in biomolecular engineering studies, the option to get an M.S. or Ph.D. is becoming ever more available in various colleges and universities.[citation needed]

1Types of biomolecules 2Nucleosides and nucleotides

o 2.1DNA and RNA structure 3Saccharides 4Lignin 5Lipids 6Amino acids

o 6.1Protein structure 6.1.1Apoenzymes 6.1.2Isoenzymes

7See also 8References 9External links

Types of biomolecules[edit]

A diverse range of biomolecules exist, including:

Small molecules : Lipids , fatty acids, glycolipids, sterols, glycerolipids Vitamins Hormones , neurotransmitters Metabolites

Monomers , oligomers and polymers:

Biomonomers Bio-oligo ! Biopolymers Polymerizationprocess

Covalent bondname between

monomers

Amino acids Oligopeptides Polypeptides, proteins (hemoglobin...) Polycondensation Peptide bond

Monosaccharides Oligosaccharides Polysaccharides (cellulose...) Polycondensation Glycosidic

bond

Isoprene Terpenes

Polyterpenes: cis-1,4-polyisoprene natural rubber and trans-1,4-polyisoprene gutta-percha

Polyaddition

Nucleotides Oligonucleotides Polynucleotides, nucleic acids (DNA, RNA)

Phosphodiester bond

Nucleosides and nucleotides[edit]Main articles: Nucleosides and Nucleotides

Nucleosides are molecules formed by attaching a nucleobase to a ribose or deoxyribose ring. Examples of these includecytidine (C), uridine (U), adenosine (A), guanosine (G), thymidine (T) and inosine (I).

Nucleosides can be phosphorylated by specific kinases in the cell, producing nucleotides. Both DNA and RNA are polymers, consisting of long, linear molecules assembled by polymerase enzymes from repeating structural units, or monomerss, of mononucleotides. DNA uses the deoxynucleotides C, G, A, and T, while RNA uses the ribonucleotides (which have an extra hydroxyl(OH) group on the pentose ring) C, G, A, and U. Modified bases are fairly common (such as with methyl groups on the base ring), as found in ribosomal RNA or transfer RNAs or for discriminating the new from old strands of DNA after replication.[1]

Each nucleotide is made of an acyclic nitrogenous base, a pentose and one to three phosphate groups. They contain carbon, nitrogen, oxygen, hydrogen and phosphorus. They serve as sources of chemical energy (adenosine triphosphateand guanosine triphosphate), participate in cellular signaling (cyclic guanosine monophosphate and cyclic adenosine monophosphate), and are incorporated into important cofactors of enzymatic reactions (coenzyme A, flavin adenine dinucleotide, flavin mononucleotide, and nicotinamide adenine dinucleotide phosphate).[2]

DNA and RNA structure[edit]Main articles: DNA and RNA structure

DNA structure is dominated by the well-known double helix formed by Watson-Crick base-pairing of C with G and A with T. This is known as B-form DNA, and is overwhelmingly the most favorable and common state of DNA; its highly specific and stable base-pairing is the basis of reliable genetic information storage. DNA can sometimes occur as single strands (often needing to be stabilized by single-strand binding proteins) or as A-form or Z-form helices, and occasionally in more complex 3D structures such as the crossover at Holliday junctions during DNA replication.[2]

Stereo 3D image of a group I intron ribozyme (PDB file 1Y0Q); gray lines show base pairs; ribbon arrows show

double-helix regions, blue to red from 5' to 3' end; white ribbon is an RNA product.

RNA, in contrast, forms large and complex 3D tertiary structures reminiscent of proteins, as well as the loose single strands with locally folded regions that constitutemessenger RNA molecules. Those RNA structures contain many stretches of A-form double helix, connected into definite 3D arrangements by single-stranded loops, bulges, and junctions.[3] Examples are tRNA, ribosomes, ribozymes, andriboswitches. These complex structures are facilitated by the fact that RNA backbone has less local flexibility than DNA but a large set of distinct conformations, apparently because of both positive and negative interactions of the extra OH on the ribose.[4]Structured RNA molecules can do highly specific binding of other molecules and can themselves be recognized specifically; in addition, they can perform enzymatic catalysis (when they are known as "ribozymes", as initially discovered by Tom Cech and colleagues.[5]

Saccharides[edit]

Monosaccharides are the simplest form of carbohydrates with only one simple sugar. They essentially contain analdehyde or ketone group in their structure.[6] The presence of an aldehyde group in a monosaccharide is indicated by the prefix aldo-. Similarly, a ketone group is denoted by the prefix keto-.[1] Examples of monosaccharides are the hexoses glucose , fructose, and galactose and pentoses, ribose, and deoxyribose Consumed fructose and glucose have different rates of gastric emptying, are differentially absorbed and have different metabolic fates, providing multiple opportunities for 2 different saccharides to differentially affect food intake. [6] Most saccharides eventually provide fuel for cellular respiration.

Disaccharides are formed when two monosaccharides, or two single simple sugars, form a bond with removal of water. They can be hydrolyzed to yield their saccharin building blocks by boiling with dilute acid or reacting them with appropriate enzymes.[1] Examples of disaccharides include sucrose, maltose, and lactose.

Polysaccharides are polymerized monosaccharides, or complex carbohydrates. They have multiple simple sugars. Examples are starch, cellulose, and glycogen. They are generally large and often have a complex branched connectivity. Because of their size, polysaccharides are not water-soluble, but their many hydroxy groups become hydrated individually when exposed to water, and some polysaccharides form thick colloidal dispersions when heated in water. [1] Shorter polysaccharides, with 3 - 10 monomers, are called oligosaccharides.[7] A fluorescent indicator-displacement molecular imprinting sensor was developed for discriminating saccharides. It successfully discriminated three brands of orange juice beverage.[8] The change in fluorescence intensity of the sensing films resulting is directly related to the saccharide concentration.[9]

Lignin[edit]

Lignin is a complex polyphenolic macromolecule composed mainly of beta-O4-aryl linkages. After cellulose, lignin is the second most abundant biopolymer and is one of the primary structural components of most plants. It contains subunits derived from p -coumaryl alcohol , coniferyl alcohol, and sinapyl alcohol [10]  and is unusual among biomolecules in that it isracemic. The lack of optical activity is due to the polymerization of lignin which occurs via free radical coupling reactions in which there is no preference for either configuration at a chiral center.

Lipids[edit]

Lipids (oleaginous) are chiefly fatty acid esters, and are the basic building blocks of biological membranes. Another biological role is energy storage (e.g., triglycerides). Most lipids consist of a polar or hydrophilic head (typically glycerol) and one to three nonpolar or hydrophobic fatty acid tails, and therefore they are amphiphilic. Fatty acids consist of unbranched chains of carbon atoms that are connected by single bonds alone (saturated fatty acids) or by both single and double bonds (unsaturated fatty acids). The chains are usually 14-24 carbon groups long, but it is always an even number.

For lipids present in biological membranes, the hydrophilic head is from one of three classes:

Glycolipids , whose heads contain an oligosaccharide with 1-15 saccharide residues.

Phospholipids , whose heads contain a positively charged group that is linked to the tail by a negatively charged phosphate group.

Sterols , whose heads contain a planar steroid ring, for example, cholesterol.

Other lipids include prostaglandins and leukotrienes which are both 20-carbon fatty acyl units synthesized from arachidonic acid. They are also known as fatty acids

Amino acids[edit]

Amino acids contain both amino and carboxylic acid functional groups. (In biochemistry, the term amino acid is used when referring to those amino acids in which the amino and carboxylate functionalities are attached to the same carbon, plusproline which is not actually an amino acid).

Modified amino acids are sometimes observed in proteins; this is usually the result of enzymatic modification after translation(protein synthesis). For example, phosphorylation of serine by kinases and dephosphorylation by phosphatases is an important control mechanism in the cell cycle. Only two amino acids other than the standard twenty are known to be incorporated into proteins during translation, in certain organisms:

Selenocysteine  is incorporated into some proteins at a UGA codon, which is normally a stop codon.

Pyrrolysine  is incorporated into some proteins at a UAG codon. For instance, in some methanogens in enzymes that are used to produce methane.

Besides those used in protein synthesis, other biologically important amino acids include carnitine (used in lipid transport within a cell), ornithine, GABA and taurine.

Protein structure[edit]The particular series of amino acids that form a protein is known as that protein's primary structure. This sequence is determined by the genetic makeup of the individual. It specifies the order of side-chain groups along the linear polypeptide "backbone".

Proteins have two types of well-classified, frequently occurring elements of local structure defined by a particular pattern ofhydrogen bonds along the backbone: alpha helix and beta sheet. Their number and arrangement is called the secondary structure of the protein. Alpha helices are regular spirals stabilized by hydrogen bonds between the backbone CO group (carbonyl) of one amino acid residue and the backbone NH group (amide) of the i+4 residue. The spiral has about 3.6 amino acids per turn, and the amino acid side chains stick out from the cylinder of the helix. Beta pleated sheets are formed by backbone hydrogen bonds between individual beta strands each of which is in an "extended", or fully stretched-out, conformation. The strands may lie parallel or antiparallel to each other, and the side-chain direction alternates above and below the sheet. Hemoglobin contains only helices, natural silk is formed of beta pleated sheets, and many enzymes have a pattern of alternating helices and beta-strands. The secondary-structure elements are connected by "loop" or "coil" regions of non-repetitive conformation, which are sometimes quite mobile or disordered but usually adopt a well-defined, stable arrangement.[11]

The overall, compact, 3D structure of a protein is termed its tertiary structure or its "fold". It is formed as result of various attractive forces like hydrogen bonding, disulfide bridges, hydrophobic interactions, hydrophilic interactions, van der Waals force etc.

When two or more polypeptide chains (either of identical or of different sequence) cluster to form a protein, quaternary structure of protein is formed. Quaternary structure is an attribute of polymeric (same-sequence chains) or heteromeric(different-sequence chains) proteins like hemoglobin, which consists of two "alpha" and two "beta" polypeptide chains.

Apoenzymes[edit]An apoenzyme (or, generally, an apoprotein) is the protein without any small-molecule cofactors, substrates, or inhibitors bound. It is often important as an inactive storage, transport, or secretory form of a protein. This is required, for instance, to protect the secretory cell from the activity of that protein. Apoenzymes becomes active enzymes on addition of a cofactor. Cofactors can be either inorganic (e.g., metal ions and iron-sulfur clusters) or organic compounds, (e.g., flavin and heme). Organic cofactors can be either prosthetic groups, which are tightly bound to an enzyme, or coenzymes, which are released from the enzyme's active site during the reaction.

Isoenzymes[edit]Isoenzymes, or isozymes, are multiple forms of an enzyme, with slightly different protein sequence and closely similar but usually not identical functions. They are either products of different genes, or else different products of alternative splicing. They may either be produced in different organs or cell types to perform the same function, or several isoenzymes may be produced in the same cell type under differential regulation to suit the needs of changing development or environment. LDH (lactate dehydrogenase) has multiple isozymes, while fetal hemoglobin is an example of a developmentally regulated isoform of a non-enzymatic protein. The relative levels of isoenzymes in blood can be used to diagnose problems in the organ of secretion.

Biomolecular engineeringFrom Wikipedia, the free encyclopedia

Biomolecular engineering is the application of engineering principles and practices to the purposeful manipulation of molecules of biological origin. Biomolecular engineers integrate knowledge of biological processes with the core knowledge of chemical engineering in order to focus on molecular level solutions to issues and problems in the life sciences related to

the environment, agriculture, energy, industry, food production, biotechnology and medicine. Biomolecular engineers purposefully manipulate carbohydrates, proteins, nucleic acids and lipids within the framework of the relation between their structure (see: nucleic acid structure, carbohydrate chemistry, protein structure,), function (see: protein function) and properties and in relation to applicability to such areas as environmental remediation, crop and live stock production, biofuel cells and biomolecular diagnostics. Fundamental attention is given to the thermodynamics and kinetics of molecular recognition in enzymes, antibodies, DNA hybridization, bio-conjugation/bio-immobilization and bioseparations. Attention is also given to the rudiments of engineered biomolecules in cell signaling, cell growth kinetics, biochemical pathway engineering and bioreactor engineering. Biomolecular engineers are leading the major shift towards understanding and controlling the molecular mechanisms that define life as we know it.

Contents  [hide] 

1 Timeline o 1.1 History o 1.2 Future

2 Basic biomolecules o 2.1 Proteins o 2.2 Carbohydrates o 2.3 Nucleic acids o 2.4 Lipids

3 Biomolecular engineering of molecules o 3.1 Recombinant DNA

3.1.1 Method 3.1.2 Applications

o 3.2 Site-directed mutagenesis 3.2.1 General procedure 3.2.2 Applications

o 3.3 Bio-immobilization and bio-conjugation o 3.4 Polymerase chain reaction

3.4.1 Biomolecular engineering techniques involved in PCR o 3.5 Enzyme-linked immunosorbent assay (ELISA)

3.5.1 Biomolecular engineering techniques involved in ELISA 4 Applications and fields

o 4.1 Biomolecular engineering in industry 4.1.1 Scale-up

o 4.2 Related industries 4.2.1 Bioengineering 4.2.2 Biochemistry 4.2.3 Biochemical engineering 4.2.4 Biotechnology 4.2.5 Bioelectrical engineering 4.2.6 Biomedical engineering

o 4.3 Chemical engineering o 4.4 Education and programs

5 See also 6 References 7 Further reading

8 External links

Timeline[edit]

History[edit]During World War II,[1] the need for large quantities of penicillin of acceptable quality brought together chemical engineers and microbiologists to focus on penicillin production. This created the right conditions to start a chain of reactions that lead to the creation of the field of biomolecular engineering. Biomolecular engineering was first defined in 1992 by the National Institutes of Health as research at the interface of chemical engineering and biology with an emphasis at the molecular level". Although first defined as research, biomolecular engineering has since become an academic discipline and a field of engineering practice. Herceptin, a humanized Mab for breast cancer treatment, became the first drug designed by a biomolecular engineering approach and was approved by the FDA. Also, Biomolecular Engineering was a former name of the journal New Biotechnology.

Future[edit]Bio-inspired technologies of the future can help explain biomolecular engineering. Looking at the Moore's law "Prediction", in the future quantum and biology-based processors are "big" technologies. With the use of biomolecular engineering, the way our processors work can be manipulated in order to function in the same sense a biological cell work. Biomolecular engineering has the potential to become one of the most important scientific disciplines because of its advancements in the analyses of gene expression patterns as well as the purposeful manipulation of many important biomolecules to improve functionality. Research in this field may lead to new drug discoveries, improved therapies, and advancement in new bioprocess technology. With the increasing knowledge of biomolecules, the rate of finding new high-value molecules including but not limited to antibodies, enzymes, vaccines, and therapeutic peptides will continue to accelerate. Biomolecular engineering will produce new designs for therapeutic drugs and high-value biomolecules for treatment or prevention of cancers, genetic diseases, and other types of metabolic diseases. Also, there is anticipation of industrial enzymes that are engineered to have desirable properties for process improvement as well the manufacturing of high-value biomolecular products at a much lower production cost. Using recombinant technology, new antibiotics that are active against resistant strains will also be produced.[2]

Basic biomolecules[edit]

Biomolecular engineering deals with the manipulation of many key biomolecules. These include, but are not limited to, proteins, carbohydrates, nucleic acids, and lipids. These molecules are the basic building blocks of life and by controlling, creating, and manipulating their form and function there are many new avenues and advantages available to society. Since every biomolecule is different, there are a number of techniques used to manipulate each one respectively.

Proteins[edit]Proteins are polymers that are made up of amino acid chains linked with peptide bonds. They have four distinct levels of structure: primary, secondary, tertiary, and quaternary. Primary structure refers to the amino acid backbone sequence. Secondary structure focuses on minor conformations that develop as a result of the hydrogen bonding between the amino acid chain. If most of the protein contains intermolecular hydrogen bonds it is said to be fibrillar, and the majority of its secondary structure will be beta sheets. However, if the majority of the orientation contains intramolecular hydrogen bonds, then the protein is referred to as globular and mostly consists of alpha helixes. There are also conformations that consist of a mix of alpha helices and beta sheets as well as a beta helixes with an alpha sheets.

The tertiary structure of proteins deal with their folding process and how the overall molecule is arranged. Finally, a quaternary structure is a group of tertiary proteins coming together and binding. With all of these levels, proteins have a wide variety of places in which they can be manipulated and adjusted. Techniques are used to affect the amino acid sequence of the protein (site directed mutagenesis), the folding and conformation of the protein, or the folding of a single tertiary protein within a quaternary protein matrix. Proteins that are the main focus of manipulation are typically enzymes. These are proteins that act as catalysts for biochemical reactions. By manipulating these catalysts, the reaction rates, products, and effects can be controlled. Enzymes and proteins are important to the biological field and research that there are specific subsets of engineering focusing only on proteins and enzymes. See protein engineering.

Carbohydrates[edit]Carbohydrates are another important biomolecule. These are polymers, called polysaccharides, which are made up of chains of simple sugars connected via glycosidic bonds. These monosaccharides consist of a five to six carbon ring that contains carbon, hydrogen, and oxygen - typically in a 1:2:1 ratio, respectively. Common monosaccharides are glucose,fructose, and ribose. When linked together monosaccharides can form disaccharides, oligosaccharides, and polysaccharides: the nomenclature is dependent on the number of monosaccharides linked together. Common dissacharides, two monosaccharides joined together, are sucrose, maltose, and lactose. Important polysaccharides, links of many monosaccharides, are cellulose, starch, and chitin.

Cellulose is a polysaccharide made up of beta 1-4 linkages between repeat glucose monomers. It is the most abundant source of sugar in nature and is a major part of the paper industry. Starch is also a polysaccharide made up of glucose monomers; however, they are connected via an alpha 1-4 linkage instead of beta. Starches, particularly amylase, are important in many industries, including the paper, cosmetic, and food. Chitin is a derivation of cellulose, possessing anacetamide group instead of an –OH on one of its carbons. Acetimide group is deacetylated the polymer chain is then calledchitosan. Both of these cellulose derivatives are a major source of research for the biomedical and food industries. They have been shown to assist with blood clotting, have antimicrobial properties, and dietary applications. A lot of engineering and research is focusing on the degree of deacetylation that provides the most effective result for specific applications.

Nucleic acids[edit]Nucleic acids are macromolecules that consist of DNA and RNA which are biopolymers consisting of chains of biomolecules. These two molecules are the genetic code and template that make life possible. Manipulation of these molecules and structures causes major changes in function and expression of other macromolecules. Nucleosides are glycosylamines containing a nucleobase bound to either ribose or deoxyribose sugar via a beta-glycosidic linkage. The sequence of the bases determine the genetic code. Nucleotides are nucleosides that are phosphorylated by specific kinases via aphosphodiester bond.[3] Nucleotides are the repeating structural units of nucleic acids. The nucleotides are made of a nitrogenous base, a pentose (ribose for RNA or deoxyribose for DNA), and three phosphate groups. See, Site-directed mutagenesis, recombinant DNA, and ELISAs.

Lipids[edit]Lipids are biomolecules that are made up of glycerol derivatives bonded with fatty acid chains. Glycerol is a simple polyolthat has a formula of C3H5(OH)3. Fatty acids are long carbon chains that have a carboxylic acid group at the end. Thecarbon chains can be either saturated with hydrogen; every carbon bond is occupied by a hydrogen atom or a single bond to another carbon in the carbon chain, or they can be unsaturated; namely, there are double bonds between the carbon atoms in the chain. Common fatty acids include lauric acid, stearic acid, and oleic acid. The study and engineering of lipids typically focuses on the manipulation of lipid membranes and encapsulation. Cellular membranes and other biological membranes typically consist of

a phospholipid bilayer membrane, or a derivative thereof. Along with the study of cellular membranes, lipids are also important molecules for energy storage. By utilizing encapsulation properties and thermodynamiccharacteristics, lipids become significant assets in structure and energy control when engineering molecules.

Biomolecular engineering of molecules[edit]

Recombinant DNA[edit]Main article: Recombinant DNA

Recombinant DNA are DNA biomolecules that contain genetic sequences that are not native to the organism’s genome. Using recombinant techniques, it is possible to insert, delete, or alter a DNA sequence precisely without depending on the location of restriction sites. There are a wide range of applications for which recombinant DNA is used.

Method[edit]

Creating recombinant DNA. After the plasmid is cleaved by restriction enzymes, ligases insert the foreign DNA

fragments into the plasmid.

The traditional method for creating recombinant DNA typically involves the use ofplasmids in the host bacteria. The plasmid contains a genetic sequence corresponding to the recognition site of a restriction endonuclease, such as EcoR1. After foreign DNA fragments, which have also been cut with the same restriction endonuclease, have been inserted into host cell, the restriction endonuclease gene is expressed by applying heat,[4] or by introducing a biomolecule, such as arabinose.[5] Upon expression, the enzyme will cleave the plasmid at its corresponding recognition site creating sticky ends on the plasmid. Ligases then joins the sticky ends to the corresponding sticky ends of the foreign DNA fragments creating a recombinant DNA plasmid.

Advances in genetic engineering have made the modification of genes in microbes quite efficient allowing constructs to be made in about a weeks worth of time. It has also made it possible to modify the organism's genome itself. Specifically, use of the genes from the bacteriophage lambda are used in recombination.[6] This mechanism, known as recombineering, utilizes the three proteins Exo, Beta, and Gam, which are created by the genes exo, bet, and gam respectively. Exo is a double stranded DNA exonuclease with 5’ to 3’ activity. It cuts the double stranded DNA leaving 3’ overhangs. Beta is a protein that binds to single stranded DNA and assists homologous recombination by promoting annealing between the homology regions of the inserted DNA and the chromosomal DNA. Gam functions to protect the DNA insert from being destroyed by nativenucleases within the cell.

Applications[edit]Recombinant DNA can be engineered for a wide variety of purposes. The techniques utilized allow for specific modification of genes making it possible to modify any biomolecule. It can be engineered

for laboratory purposes, where it can be used to analyze genes in a given organism. In the pharmaceutical industry, proteins can be modified using recombination techniques. Some of these proteins include human insulin. Recombinant insulin is synthesized by inserting the human insulin gene into E. coli, which then produces insulin for human use.[7][8] Other proteins, such as human growth hormone,[9] factor VIII, and hepatitis B vaccine are produced using similar means. Recombinant DNA can also be used for diagnostic methods involving the use of the ELISA method. This makes it possible to engineer antigens, as well as the enzymes attached, to recognize different substrates or be modified for bioimmobilization. Recombinant DNA is also responsible for many products found in the agricultural industry. Genetically modified food, such as golden rice,[10] has been engineered to have increased production of vitamin A for use in societies and cultures where dietary vitamin A is scarce. Other properties that have been engineered into crops include herbicide-resistance[11] and insect-resistance.[12]

Site-directed mutagenesis[edit]Site-directed mutagenesis is a technique that has been around since the 1970s. The early days of research in this field yielded discoveries about the potential of certain chemicals such as bisulfite and aminopurine to change certain bases in a gene. This research continued, and other processes were developed to create certain nucleotide sequences on a gene, such as the use of restriction enzymes to fragment certain viral strands and use them as primers for bacterial plasmids. The modern method, developed by Michael Smith in 1978, uses an oligonucleotide that is complementary to a bacterial plasmid with a single base pair mismatch or a series of mismatches. [13]

General procedure[edit]Site directed mutagenesis is a valuable technique that allows for the replacement of a single base in an oligonucleotide or gene. The basics of this technique involve the preparation of a primer that will be a complementary strand to a wild type bacterial plasmid. This primer will have a base pair mismatch at the site where the replacement is desired. The primer must also be long enough such that the primer will anneal to the wild type plasmid. After the primer anneals, a DNA polymerase will complete the primer. When the bacterial plasmid is replicated, the mutated strand will be replicated as well. The same technique can be used to create a gene insertion or deletion. Often, an antibiotic resistant gene is inserted along with the modification of interest and the bacteria are cultured on an antibiotic medium. The bacteria that were not successfully mutated will not survive on this medium, and the mutated bacteria can easily be cultured.

This animation shows the basic steps of site directed mutagenesis, where X-Y is the desired base pair

replacement of T-A.

Applications[edit]Site-directed mutagenesis can be useful for many different reasons. A single base pair replacement, could change a codon, and thus replace an amino acid in a protein. This is useful for studying the

way certain proteins behave. It is also useful because enzymes can be purposefully manipulated by changing certain amino acids. If an amino acid is changed that is in close proximity to the active site, the kinetic parameters may change drastically, or the enzyme might behave in a different way. Another application of site directed mutagenesis is exchanging an amino acid residue far from the active site with a lysine residue or cysteine residue. These amino acids make it easier to covalently bond the enzyme to a solid surface, which allows for enzyme re-use and use of enzymes in continuous processes. Sometimes, amino acids with non-natural functional groups (such as ketones and azides) are added to proteins[14] These additions may be for ease of bioconjugation, or to study the effects of amino acid changes on the form and function of the proteins. The coupling of site directed mutagenesis and PCR are being utilized to reduce interleukin-6 activity in cancerous cells.[15] The bacteria bacillus subtilis is often used in site directed mutagenesis.[16] The bacteria secretes an enzyme called subtilisin through the cell wall. Biomolecular engineers can purposely manipulate this gene to essentially make the cell a factory for producing whatever protein the insertion in the gene codes.

Bio-immobilization and bio-conjugation[edit]Bio-immobilization and bio-conjugation is the purposeful manipulation of a biomolecule’s mobility by chemical or physical means to obtain a desired property. Immobilization of biomolecules allows exploiting characteristics of the molecule under controlled environments. For example [17] , the immobilization of glucose oxidase on calcium alginate gel beads can be used in a bioreactor. The resulting product will not need purification to remove the enzyme because it will remain linked to the beads in the column. Examples of types of biomolecules that are immobilized are enzymes, organelles, and complete cells. Biomolecules can be immobilized using a range of techniques. The most popular are physical entrapment, adsorption, and covalent modification.

Physical entrapment[18] - the use of a polymer to contain the biomolecule in a matrix without chemical modification. Entrapment can be between lattices of polymer, known as gel entrapment, or within micro-cavities of synthetic fibers, known as fiber entrapment. Examples include entrapment of enzymes such as glucose oxidase in gel column for use as abioreactor. Important characteristic with entrapment is biocatalyst remains structurally unchanged, but creates large diffusion barriers for substrates.

Adsorption - immobilization of biomolecules due to interaction between the biomolecule and groups on support. Can be physical adsorption, ionic bonding, or metal binding chelation. Such techniques can be performed under mild conditions and relatively simple, although the linkages are highly dependent upon pH, solvent and temperature. Examples include enzyme-linked immunosorbent assays.

Covalent modification- involves chemical reactions between certain functional groups and matrix. This method forms stable complex between biomolecule and matrix and is suited for mass production. Due to the formation of chemical bond to functional groups, loss of activity can occur. Examples of chemistries used are DCC coupling[19] PDC coupling and EDC/NHS coupling, all of which take advantage of the reactive amines on the biomolecule’s surface.

Because immobilization restricts the biomolecule, care must be given to ensure that functionality is not entirely lost. Variables to consider are pH,[20] temperature, solvent choice, ionic strength, orientation of active sites due to conjugation. For enzymes, the conjugation will lower the kinetic rate due to a change in the 3-dimensional structure, so care must be taken to ensure functionality is not lost. Bio-immobilization is used in technologies such as diagnostic bioassays, biosensors,ELISA, and bioseparations. Interleukin (IL-6) can also be bioimmobilized on biosensors. The ability to observe these changes in IL-6 levels is important in diagnosing an illness. A cancer patient will have elevated IL-6 level and monitoring those levels will allow the physician to watch the disease progress. A direct immobilization of IL-6 on the surface of a biosensor offers a fast alternative to ELISA.[21]

Polymerase chain reaction[edit]Main article: Polymerase chain reaction

Polymerase chain reaction. There are three main steps involved in PCR. In the first step, the double stranded

DNA strands are "melted" or denatured forming single stranded DNA. Next, primers, which have been

designed to target a specific gene sequence on the DNA, anneal to the single stranded DNA. Lastly, DNA

polymerase synthesizes a new DNA strand complimentary to the original DNA. These three steps are repeated

multiple times until the desired number of copies are made.

The polymerase chain reaction (PCR) is a scientific technique that is used to replicate a piece of a DNA molecule by several orders of magnitude. PCR implements a cycle of repeated heated and cooling known as thermal cycling along with the addition of DNA primers and DNA polymerases to selectively replicate the DNA fragment of interest. The technique was developed by Kary Mullis in 1983 while working for the Cetus Corporation.Mullis would go on to win the Nobel Prize in Chemistry in 1993 as a result of the impact thatPCR had in many areas such as DNA cloning, DNA sequencing, and gene analysis.[22]

Biomolecular engineering techniques involved in PCR[edit]A number of biomolecular engineering strategies have played a very important role in the development and practice of PCR. For instance a crucial step in insuring the accurate replication of the desired DNA fragment is the creation of the correct DNA primer. The most common method of primer synthesis is by the phosphoramidite method. This method includes the biomolecular engineering of a number of molecules to attain the desired primer sequence. The most prominent biomolecular engineering technique seen in this primerdesign method is the initial bioimmobilization of a nucleotide to a solid support. This step is commonly done via the formation of a covalent bond between the 3’-hydroxy group of the first nucleotide of the primer and the solid support material. [23]

Furthermore, as the DNA primer is created certain functional groups of nucleotides to be added to the growing primer require blocking to prevent undesired side reactions. This blocking of functional groups as well as the subsequent de-blocking of the groups, coupling of subsequent nucleotides, and eventual cleaving from the solid support[23] are all methods of manipulation of biomolecules that can be attributed to biomolecular engineering. The increase in interleukin levels is directly proportional to the increased death rate in breast cancer patients. PCR paired with Western blotting and ELISA help define the relationship between cancer cells and IL-6. [24]

Enzyme-linked immunosorbent assay (ELISA)[edit]Main article: ELISA

Enzyme-linked immunosorbent assay is an assay that utilizes the principle of antibody-antigen recognition to test for the presence of certain substances. The three main types ofELISA tests which are indirect ELISA, sandwich ELISA, and competitive ELISA all rely on the fact that antibodies have an affinity for only one specific antigen. Furthermore, theseantigens or antibodies can be attached to enzymes which can react to create a colorimetric result indicating the presence of the antibody or antigen of interest.[25] Enzyme linked immunosorbent assays are used most commonly as diagnostic tests to detect HIV antibodies in blood samples to test for HIV, human chorionic gonadotropin molecules in urine to indicate pregnancy, and Mycobacterium tuberculosis antibodies in blood to test patients for tuberculosis. Furthermore, ELISA is also widely used as a toxicology screen to test people's serum for the presence of illegal drugs.

Biomolecular engineering techniques involved in ELISA[edit]Although there are three different types of solid state enzyme-linked immunosorbent assays, all three types begin with the bioimmobilization of either an antibody or antigen to a surface. This bioimmobilization is the first instance of biomolecular engineering that can be seen in ELISA implementation. This step can be performed in a number of ways including a covalent linkage to a surface which may be coated with protein or another substance. The bioimmobilization can also be performed via hydrophobic interactions between the molecule and the surface. Because there are many different types of ELISAs used for many different purposes the biomolecular engineering that this step requires varies depending on the specific purpose of the ELISA.

Another biomolecular engineering technique that is used in ELISA development is the bioconjugation of an enzyme to either an antibody or antigen depending on the type of ELISA. There is much to consider in this enzyme bioconjugation such as avoiding interference with the active site of the enzyme as well as the antibody binding site in the case that the antibody is conjugated with enzyme. This bioconjugation is commonly performed by creating crosslinks between the two molecules of interest and can require a wide variety of different reagents depending on the nature of the specific molecules.[26]

Interleukin (IL-6) is a signaling protein that has been known to be present during an immune response. The use of the sandwich type ELISA quantifies the presence of this cytokine within spinal fluid or bone marrow samples.[27]

Applications and fields[edit]

Biomolecular engineering in industry[edit]

Graph showing number of biotech companies per country[28]

Graph showing percentages of biotech firms by application [29]

Biomolecular engineering is an extensive discipline with applications in many different industries and fields. As such, it is difficult to pinpoint a general perspective on the Biomolecular engineering profession. The biotechnology industry, however, provides an adequate representation. The biotechnology industry, or biotech industry, encompasses all firms that use biotechnology to produce goods or services or to perform biotechnology research and development. [28] In this way, it encompasses many of the industrial applications of the biomolecular engineering discipline. By examination of the biotech industry, it can be gathered that the principal leader of the industry is the United States, followed by France and Spain.[28] It is also true that the focus of the biotechnology industry and the application of biomolecular engineering is primarily clinical and medical. People are willing to pay for good health, so most of the money directed towards the biotech industry stays in health-related ventures.[citation needed]

Scale-up[edit]Scaling up a process involves using data from an experimental-scale operation (model or pilot plant) for the design of a large (scaled-up) unit, of commercial size. Scaling up is a crucial part of commercializing a process. For example, insulinproduced by genetically modified Escherichia coli bacteria was initialized on a lab-scale, but to be made commercially viable had to be scaled up to an industrial level. In order to achieve this scale-up a lot of lab data had to be used to design commercial sized units. For example, one of the steps in insulin production involves the crystallization of high purity glargin insulin.[30] In order to achieve this process on a large scale we want to keep the Power/Volume ratio of both the lab-scale and large-scale crystallizers the same in order to achieve homogeneous mixing.[31] We also assume the lab-scale crystallizer has geometric similarity to the large-scale crystallizer. Therefore,

P/V α Ni3di

3

where di= crystallizer impeller diameterNi= impeller rotation rate

Related industries[edit]Bioengineering[edit]Main article: Biological engineering

A broad term encompassing all engineering applied to the life sciences. This field of study utilizes the principles of biologyalong with engineering principles to create marketable products. Some bioengineering applications include:

Biomimetics  - The study and development of synthetic systems that mimic the form and function of natural biologically produced substances and processes.

Bioprocess engineering  - The study and development of process equipment and optimization that aids in the production of many products such as food and pharmaceuticals.

Industrial microbiology  - The implementation of microorganisms in the production of industrial products such as food andantibiotics. Another common application of industrial microbiology is the treatment of wastewater in chemical plants via utilization of certain microorganisms.

Biochemistry[edit]Main article: Biochemistry

Biochemistry is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemical processes govern all living organisms and living processes and the field of biochemistry seeks to understand and manipulate these processes.

Biochemical engineering[edit]Main article: Biochemical engineering

Biocatalysis  – Chemical transformations using enzymes. Bioseparations  – Separation of biologically active molecules. Thermodynamics  and Kinetics (chemistry) – Analysis of reactions involving cell growth and

biochemicals. Bioreactor  design and analysis – Design of reactors for performing biochemical transformations.

Biotechnology[edit]Main article: Biotechnology

Biomaterials  – Design, synthesis and production of new materials to support cells and tissues. Genetic engineering  – Purposeful manipulation of the genomes of organisms to produce new

phenotypic traits. Bioelectronics , Biosensor and Biochip – Engineered devices and systems to measure, monitor

and control biological processes. Bioprocess engineering  – Design and maintenance of cell-based and enzyme-based processes

for the production of fine chemicals and pharmaceuticals.

Bioelectrical engineering[edit]Main article: Bioelectric

Bioelectrical engineering involves the electrical fields generated by living cells or organisms. Examples include the electric potential developed between muscles or nerves of the body. This

discipline requires knowledge in the fields of electricity andbiology to understand and utilize these concepts to improve or better current bioprocesses or technology.

Bioelectrochemistry  - Chemistry concerned with electron/proton transport throughout the cell Bioelectronics  - Field of research coupling biology and electronics

Biomedical engineering[edit]Main article: Biomedical engineering

Biomedical engineering is a sub category of bioengineering that uses many of the same principles but focuses more on the medical applications of the various engineering developments. Some applications of biomedical engineering include:

Biomaterials  - Design of new materials for implantation in the human body and analysis of their effect on the body.

Cellular engineering  – Design of new cells using recombinant DNA and development of procedures to allow normal cells to adhere to artificial implanted biomaterials

Tissue engineering  – Design of new tissues from the basic biological building blocks to form new tissues

Artificial organs  – Application of tissue engineering to whole organs Medical imaging  – Imaging of tissues using CAT scan, MRI, ultrasound, x-ray or other

technologies Medical Optics and Lasers – Application of lasers to medical diagnosis and treatment Rehabilitation engineering  – Design of devices and systems used to aid the disabled Man-machine interfacing - Control of surgical robots and remote diagnostic and therapeutic

systems using eye tracking, voice recognition and muscle and brain wave controls Human factors and ergonomics  – Design of systems to improve human performance in a wide

range of applications

Chemical engineering[edit]Main article: Chemical engineering

Chemical engineering is the processing of raw materials into chemical products. It involves preparation of raw materials to produce reactants, the chemical reaction of these reactants under controlled conditions, the separation of products, the recycle of byproducts, and the disposal of wastes. Each step involves certain basic building blocks called “unit operations,” such as extraction, filtration, and distillation.[32] These unit operations are found in all chemical processes. Biomolecular engineering is a subset of Chemical Engineering that applies these same principles to the processing of chemical substances made by living organisms.

Education and programs[edit]The discipline of biomolecular engineering has become ever more prevalent with the better understanding and advancement of current sciences and technologies. In previous years, biomolecular engineering was not a well-known career path, but the growth in popularity of this subject has resulted in new programs offered to undergraduate and graduate students. [citation needed]

Newly developed and offered undergraduate programs across the United States, often coupled to the chemical engineering program, allow students to achieve a B.S. degree. According to ABET (Accreditation Board for Engineering and Technology), biomolecular engineering curricula "must provide thorough grounding in the basic sciences including chemistry, physics, and biology, with some content at an advanced level… [and] engineering application of these basic sciences to design, analysis, and control, of chemical, physical, and/or biological processes."[33] Common curricula consist of major engineering courses including transport, thermodynamics, separations,

and kinetics, with additions of life sciencescourses including biology and biochemistry, and including specialized biomolecular courses focusing on cell biology, nano- and biotechnology, biopolymers, etc.[34]

To further education in biomolecular engineering studies, the option to get an M.S. or Ph.D. is becoming ever more available in various colleges and universities

List of biomoleculesFrom Wikipedia, the free encyclopedia

This is a list of articles that describe particular biomolecules or types of biomolecules.

Contents :

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z See also

A[edit]

For substances with an A- or α- prefix such as α-amylase, please see the parent page (in this case Amylase).

A23187  (Calcimycin, Calcium Ionophore) Abamectine Abietic acid Acetic acid

Acetylcholine Actin Actinomycin D Adenosine Adenosine diphosphate  (ADP) Adenosine monophosphate  (AMP) Adenosine triphosphate  (ATP) Adenylate cyclase Adonitol Adrenaline , epinephrine Adrenocorticotropic hormone  (ACTH) Aequorin Aflatoxin Agar Alamethicin Alanine Albumins Aldosterone Aleurone Alpha-amanitin Allantoin Allethrin α-Amanatin, see Alpha-amanitin Amino acid Amylase  (also see α-amylase) Anabolic steroid Anethole Angiotensinogen Anisomycin Antidiuretic hormone  (ADH) Arabinose Arginine Ascomycin Ascorbic acid  (vitamin C) Asparagine Aspartic acid Asymmetric dimethylarginine Atrial-natriuretic peptide  (ANP) Auxin Avidin Azadirachtin  A – C35H44O16

B[edit]

Bacteriocin Beauvericin Bicuculline Bilirubin

Biopolymer Biotin  (Vitamin H) Brefeldin A Brassinolide Brucine

C[edit]

Cadaverine Caffeine Calciferol  (Vitamin D) Calcitonin Calmodulin Calmodulin Calreticulin Camphor  - (C10H16O) Cannabinol  - (C21H26O2) Capsaicin Carbohydrase Carbohydrate Carnitine Carrageenan Casein Caspase Cellulase Cellulose  - (C6H10O5)x

Cerulenin Cetrimonium bromide  (Cetrimide) - C19H42BrN Chelerythrine Chromomycin A3 Chaparonin Chitin α-Chloralose Chlorophyll Cholecystokinin  (CCK) Cholesterol Choline Chondroitin sulfate Cinnamaldehyde Citral Citric acid Citrinin Citronellal Citronellol Citrulline Cobalamin  (vitamin B12) Coenzyme Coenzyme Q

Colchicine Collagen Coniine Corticosteroid Corticosterone Corticotropin-releasing hormone  (CRH) Cortisol Creatine Creatine kinase Crystallin α-Cyclodextrin Cyclodextrin glycosyltransferase Cyclopamine Cyclopiazonic acid Cysteine Cystine Cytidine Cytochalasin Cytochalasin E Cytochrome Cytochrome C Cytochrome c oxidase Cytochrome c peroxidase Cytokine Cytosine  – C4H5N3O

D[edit]

Deoxycholic acid DON  (DeoxyNivalenol) Deoxyribofuranose Deoxyribose Deoxyribose nucleic acid  (DNA) Dextran Dextrin DNA Dopamine

E[edit]

Enzyme Ephedrine Epinephrine  – C9H13NO3

Erucic acid  – CH3(CH2)7CH=CH(CH2)11COOH Erythritol Erythropoietin  (EPO) Estradiol Eugenol

F[edit]

Fatty acid Fibrin Fibronectin Folic acid  (Vitamin M) Follicle stimulating hormone  (FSH) Formaldehyde Formic acid Formnoci Fructose Fumonisin B1

G[edit]

Galactose Gamma globulin Gamma-aminobutyric acid Gamma-butyrolactone Gamma-hydroxybutyrate  (GHB) Gastrin Gelatin Geraniol Globulin Glucagon Glucosamine Glucose  – C6H12O6

Glucose oxidase Glutamic acid Glutamine Glutathione Gluten Glycerin  (glycerol) Glycine Glycogen Glycolic acid

Glycoprotein Gonadotropin-releasing hormone  (GnRH) Granzyme Green fluorescent protein Growth hormone Growth hormone-releasing hormone  (GHRH) GTPase Guanine Guanosine Guanosine triphosphate  (+GTP)

H[edit]

[[Haptog

obin]]

Hematoxylin Heme Hemerythrin Hemocyanin Hemoglobin Hemoprotein Heparan sulfate High density lipoprotein , HDL Histamine Histidine Histone Histone methyltransferase HLA antigen Homocysteine Hormone human chorionic gonadotropin  (hCG) Human growth hormone Hyaluronate Hyaluronidase Hydrogen peroxide 5-Hydroxymethylcytosine Hydroxyproline 5-Hydroxytryptamine

I[edit]

Indigo dye Indole Inosine Inositol Insulin Insulin-like growth factor Integral membrane protein Integrase Integrin Intein Interferon Inulin Ionomycin Ionone Isoleucine Iron-sulfur cluster

J[edit]

This section is empty. You can help 

by adding to it. (July 2010)

K[edit]

K252a K252b KT5720 KT5823 Keratin Kinase

L[edit]

For substances with an l- or L- prefix such as L-alanine or DL-alanine, please see the parent page (in this case alanine).

Lactase Lactic acid Lactose Lanolin Lauric acid Leptin Leptomycin B Leucine Lignin Limonene Linalool Linoleic acid Linolenic acid Lipase Lipid Lipid anchored protein Lipoamide Lipoprotein Low density lipoprotein , LDL Luteinizing hormone  (LH) Lycopene Lysine Lysozyme

M[edit]

Malic acid Maltose

Melatonin Membrane protein Metalloprotein Metallothionein Methionine Mimosine Mithramycin A Mitomycin C Monomer Morphine Mycophenolic acid Myoglobin Myosin

N[edit]

Natural phenols Nucleic Acid

O[edit]

Ochratoxin A Oestrogens Oligopeptide Oligomycin Orcin Orexin Ornithine Oxalic acid Oxidase Oxytocin

P[edit]

p53 PABA Paclitaxel Palmitic acid Pantothenic acid  (vitamin B5) parathyroid hormone  (PTH) Paraprotein Pardaxin Parthenolide Patulin Paxilline Penicillic acid Penicillin

Penitrem A Peptidase Pepsin Peptide Perimycin Peripheral membrane protein Perosamine Phenethylamine Phenylalanine Phosphagen phosphatase Phospholipid Phenylalanine Phytic acid Plant hormones Polypeptide Polyphenols Polysaccharides Porphyrin Prion Progesterone Prolactin  (PRL) Proline Propionic acid Protamine Protease Protein Proteinoid Putrescine Pyrethrin Pyridoxine  or pyridoxamine (Vitamin B6) Pyrrolysine Pyruvic acid

Q[edit]

Quinidine Quinine Quinone

R[edit]

Radicicol Raffinose Renin Retinene Retinol  (Vitamin A) Rhodopsin  (visual purple)

Riboflavin  (vitamin B2) Ribofuranose , Ribose Ribozyme Ricin RNA  - Ribonucleic acid RuBisCO

S[edit]

Safrole Salicylaldehyde Salicylic acid Salvinorin-A  – C23H28O8

Saponin Secretin Selenocysteine Selenomethionine Selenoprotein Serine Serine kinase Serotonin Skatole Signal recognition particle Somatostatin Sorbic acid Squalene Staurosporin Stearic acid Sterigmatocystin Sterol Strychnine Sucrose  (sugar) Sugars  (in general) superoxide

T[edit]

T2 Toxin Tannic acid Tannin Tartaric acid Taurine Tetrodotoxin Thaumatin Topoisomerase Tyrosine kinase Taurine Testosterone

Tetrahydrocannabinol  (THC) Tetrodotoxin Thapsigargin Thaumatin Thiamine  (vitamin B1) – C12H17ClN4OS·HCl Threonine Thrombopoietin Thymidine Thymine Triacsin C Thyroid-stimulating hormone  (TSH) Thyrotropin-releasing hormone  (TRH) Thyroxine  (T4) Tocopherol  (Vitamin E) Topoisomerase Triiodothyronine  (T3) Transmembrane receptor Trichostatin A Trophic hormone Trypsin Tryptophan Tubulin Tunicamycin Tyrosine

U[edit]

Ubiquitin Uracil Urea Urease Uric acid  – C5H4N4O3

Uridine

V[edit]

Valine Valinomycin Vanabins Vasopressin Verruculogen Vitamins  (in general) Vitamin A  (retinol) Vitamin B  ()

Vitamin B 1 (thiamine) Vitamin B 2 (riboflavin) Vitamin B 3 (niacin or nicotinic acid) Vitamin B 4 (adenine)

Vitamin B 5 (pantothenic acid) Vitamin B 6 (pyridoxine or pyridoxamine) Vitamin B 12 (cobalamin)

Vitamin C  (ascorbic acid) Vitamin D  (calciferol) Vitamin E  (tocopherol) Vitamin F Vitamin H  (biotin) Vitamin K  (naphthoquinone) Vitamin M  (folic acid)

W[edit]

Water Wortmannin

X[edit]

Xylose

Y[edit]

Z[edit]

Zearalenone

List of biomoleculesFrom Wikipedia, the free encyclopedia

This is a list of articles that describe particular biomolecules or types of biomolecules.

Contents :

A B C D E F G H I J K L M N O P Q

R S T U V W X Y Z See also

A[edit]

For substances with an A- or α- prefix such as α-amylase, please see the parent page (in this case Amylase).

A23187  (Calcimycin, Calcium Ionophore) Abamectine Abietic acid Acetic acid Acetylcholine Actin Actinomycin D Adenosine Adenosine diphosphate  (ADP) Adenosine monophosphate  (AMP) Adenosine triphosphate  (ATP) Adenylate cyclase Adonitol Adrenaline , epinephrine Adrenocorticotropic hormone  (ACTH) Aequorin Aflatoxin Agar Alamethicin Alanine Albumins Aldosterone Aleurone Alpha-amanitin Allantoin Allethrin α-Amanatin, see Alpha-amanitin Amino acid Amylase  (also see α-amylase) Anabolic steroid Anethole Angiotensinogen Anisomycin Antidiuretic hormone  (ADH)

Arabinose Arginine Ascomycin Ascorbic acid  (vitamin C) Asparagine Aspartic acid Asymmetric dimethylarginine Atrial-natriuretic peptide  (ANP) Auxin Avidin Azadirachtin  A – C35H44O16

B[edit]

Bacteriocin Beauvericin Bicuculline Bilirubin Biopolymer Biotin  (Vitamin H) Brefeldin A Brassinolide Brucine

C[edit]

Cadaverine Caffeine Calciferol  (Vitamin D) Calcitonin Calmodulin Calmodulin Calreticulin Camphor  - (C10H16O) Cannabinol  - (C21H26O2) Capsaicin Carbohydrase Carbohydrate Carnitine Carrageenan Casein Caspase Cellulase Cellulose  - (C6H10O5)x

Cerulenin Cetrimonium bromide  (Cetrimide) - C19H42BrN Chelerythrine Chromomycin A3

Chaparonin Chitin α-Chloralose Chlorophyll Cholecystokinin  (CCK) Cholesterol Choline Chondroitin sulfate Cinnamaldehyde Citral Citric acid Citrinin Citronellal Citronellol Citrulline Cobalamin  (vitamin B12) Coenzyme Coenzyme Q Colchicine Collagen Coniine Corticosteroid Corticosterone Corticotropin-releasing hormone  (CRH) Cortisol Creatine Creatine kinase Crystallin α-Cyclodextrin Cyclodextrin glycosyltransferase Cyclopamine Cyclopiazonic acid Cysteine Cystine Cytidine Cytochalasin Cytochalasin E Cytochrome Cytochrome C Cytochrome c oxidase Cytochrome c peroxidase Cytokine Cytosine  – C4H5N3O

D[edit]

Deoxycholic acid DON  (DeoxyNivalenol)

Deoxyribofuranose Deoxyribose Deoxyribose nucleic acid  (DNA) Dextran Dextrin DNA Dopamine

E[edit]

Enzyme Ephedrine Epinephrine  – C9H13NO3

Erucic acid  – CH3(CH2)7CH=CH(CH2)11COOH Erythritol Erythropoietin  (EPO) Estradiol Eugenol

F[edit]

Fatty acid Fibrin Fibronectin Folic acid  (Vitamin M) Follicle stimulating hormone  (FSH) Formaldehyde Formic acid Formnoci Fructose Fumonisin B1

G[edit]

Galactose Gamma globulin Gamma-aminobutyric acid Gamma-butyrolactone Gamma-hydroxybutyrate  (GHB) Gastrin Gelatin Geraniol Globulin Glucagon Glucosamine Glucose  – C6H12O6

Glucose oxidase

Glutamic acid Glutamine Glutathione Gluten Glycerin  (glycerol) Glycine Glycogen Glycolic acid

Glycoprotein Gonadotropin-releasing hormone  (GnRH) Granzyme Green fluorescent protein Growth hormone Growth hormone-releasing hormone  (GHRH) GTPase Guanine Guanosine Guanosine triphosphate  (+GTP)

H[edit]

[[Haptog

obin]]

Hematoxylin Heme Hemerythrin Hemocyanin Hemoglobin Hemoprotein Heparan sulfate High density lipoprotein , HDL Histamine Histidine Histone Histone methyltransferase HLA antigen Homocysteine Hormone human chorionic gonadotropin  (hCG) Human growth hormone Hyaluronate Hyaluronidase Hydrogen peroxide 5-Hydroxymethylcytosine Hydroxyproline 5-Hydroxytryptamine

I[edit]

Indigo dye Indole Inosine Inositol Insulin Insulin-like growth factor Integral membrane protein Integrase Integrin Intein Interferon Inulin Ionomycin Ionone Isoleucine Iron-sulfur cluster

J[edit]

This section is empty. You can help 

by adding to it. (July 2010)

K[edit]

K252a K252b KT5720 KT5823 Keratin Kinase

L[edit]

For substances with an l- or L- prefix such as L-alanine or DL-alanine, please see the parent page (in this case alanine).

Lactase Lactic acid Lactose Lanolin Lauric acid Leptin Leptomycin B Leucine Lignin

Limonene Linalool Linoleic acid Linolenic acid Lipase Lipid Lipid anchored protein Lipoamide Lipoprotein Low density lipoprotein , LDL Luteinizing hormone  (LH) Lycopene Lysine Lysozyme

M[edit]

Malic acid Maltose Melatonin Membrane protein Metalloprotein Metallothionein Methionine Mimosine Mithramycin A Mitomycin C Monomer Morphine Mycophenolic acid Myoglobin Myosin

N[edit]

Natural phenols Nucleic Acid

O[edit]

Ochratoxin A Oestrogens Oligopeptide Oligomycin Orcin Orexin Ornithine

Oxalic acid Oxidase Oxytocin

P[edit]

p53 PABA Paclitaxel Palmitic acid Pantothenic acid  (vitamin B5) parathyroid hormone  (PTH) Paraprotein Pardaxin Parthenolide Patulin Paxilline Penicillic acid Penicillin Penitrem A Peptidase Pepsin Peptide Perimycin Peripheral membrane protein Perosamine Phenethylamine Phenylalanine Phosphagen phosphatase Phospholipid Phenylalanine Phytic acid Plant hormones Polypeptide Polyphenols Polysaccharides Porphyrin Prion Progesterone Prolactin  (PRL) Proline Propionic acid Protamine Protease Protein Proteinoid Putrescine

Pyrethrin Pyridoxine  or pyridoxamine (Vitamin B6) Pyrrolysine Pyruvic acid

Q[edit]

Quinidine Quinine Quinone

R[edit]

Radicicol Raffinose Renin Retinene Retinol  (Vitamin A) Rhodopsin  (visual purple) Riboflavin  (vitamin B2) Ribofuranose , Ribose Ribozyme Ricin RNA  - Ribonucleic acid RuBisCO

S[edit]

Safrole Salicylaldehyde Salicylic acid Salvinorin-A  – C23H28O8

Saponin Secretin Selenocysteine Selenomethionine Selenoprotein Serine Serine kinase Serotonin Skatole Signal recognition particle Somatostatin Sorbic acid Squalene Staurosporin Stearic acid

Sterigmatocystin Sterol Strychnine Sucrose  (sugar) Sugars  (in general) superoxide

T[edit]

T2 Toxin Tannic acid Tannin Tartaric acid Taurine Tetrodotoxin Thaumatin Topoisomerase Tyrosine kinase Taurine Testosterone Tetrahydrocannabinol  (THC) Tetrodotoxin Thapsigargin Thaumatin Thiamine  (vitamin B1) – C12H17ClN4OS·HCl Threonine Thrombopoietin Thymidine Thymine Triacsin C Thyroid-stimulating hormone  (TSH) Thyrotropin-releasing hormone  (TRH) Thyroxine  (T4) Tocopherol  (Vitamin E) Topoisomerase Triiodothyronine  (T3) Transmembrane receptor Trichostatin A Trophic hormone Trypsin Tryptophan Tubulin Tunicamycin Tyrosine

U[edit]

Ubiquitin

Uracil Urea Urease Uric acid  – C5H4N4O3

Uridine

V[edit]

Valine Valinomycin Vanabins Vasopressin Verruculogen Vitamins  (in general) Vitamin A  (retinol) Vitamin B  ()

Vitamin B 1 (thiamine) Vitamin B 2 (riboflavin) Vitamin B 3 (niacin or nicotinic acid) Vitamin B 4 (adenine) Vitamin B 5 (pantothenic acid) Vitamin B 6 (pyridoxine or pyridoxamine) Vitamin B 12 (cobalamin)

Vitamin C  (ascorbic acid) Vitamin D  (calciferol) Vitamin E  (tocopherol) Vitamin F Vitamin H  (biotin) Vitamin K  (naphthoquinone) Vitamin M  (folic acid)

W[edit]

Water Wortmannin

X[edit]

Xylose

Y[edit]

Z[edit]

Zearalenone

MetabolismFrom Wikipedia, the free encyclopedia

"Cell metabolism" redirects here. For the journal, see Cell Metabolism.

For the architectural movement, see Metabolism (architecture).

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Structure of adenosine triphosphate(ATP), a central intermediate in energy metabolism

Metabolism (from Greek: μεταβολή metabolē, "change") is the set of life-sustaining chemical transformations within the cells of living organisms. Theseenzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to all chemical reactions that occur in living organisms, includingdigestion and the transport of substances into and between different cells, in which case the set of reactions within the cells is called intermediary metabolism or intermediate metabolism.

Metabolism is usually divided into two categories: catabolism, the breaking down of organic matter by way of cellular respiration, and anabolism, thebuilding up of components of cells such as proteins and nucleic acids. Usually, breaking down releases energy and building up consumes energy.

The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energythat will not occur by themselves, by coupling them to spontaneous reactionsthat release energy. Enzymes act as catalysts that allow the reactions to proceed more rapidly. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or to signals from other cells.

The metabolic system of a particular organism determines which substances it will find nutritious and which poisonous. For example, some prokaryotes usehydrogen sulfide as a nutrient, yet this gas is poisonous to animals.[1] The speed of metabolism, the metabolic rate, influences how much food an organism will require, and also affects how it is able to obtain that food.

A striking feature of metabolism is the similarity of the basic metabolic pathways and components between even vastly different species.[2] For example, the set ofcarboxylic acids that are best known as the intermediates in the citric acid cycle are present in all known organisms, being found in species as diverse as the unicellularbacterium Escherichia coli and huge multicellular organisms like elephants.[3] These striking similarities in metabolic pathways are likely due to their early appearance inevolutionary history, and their retention because of their efficacy.[4][5]

Contents  [hide] 

1 Key biochemicals o 1.1 Amino acids and proteins o 1.2 Lipids o 1.3 Carbohydrates o 1.4 Nucleotides o 1.5 Coenzymes o 1.6 Minerals and cofactors

2 Catabolism o 2.1 Digestion o 2.2 Energy from organic compounds

3 Energy transformations o 3.1 Oxidative phosphorylation o 3.2 Energy from inorganic compounds o 3.3 Energy from light

4 Anabolism o 4.1 Carbon fixation o 4.2 Carbohydrates and glycans o 4.3 Fatty acids, isoprenoids and steroids o 4.4 Proteins o 4.5 Nucleotide synthesis and salvage

5 Xenobiotics and redox metabolism 6 Thermodynamics of living organisms 7 Regulation and control 8 Evolution 9 Investigation and manipulation 10 History 11 See also 12 References 13 Further reading 14 External links

Key biochemicals[edit]Further information: Biomolecule, cell (biology) and biochemistry

Structure of a triacylglycerol lipid

Most of the structures that make up animals, plants and microbes are made from three basic classes of molecule: amino acids, carbohydrates and lipids(often called fats). As these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or by breaking them down and using them as a source of energy, by their digestion. These biochemicals can be joined together to make polymerssuch as DNA and proteins, essential macromolecules of life.

Type of molecule

Name ofmonomer forms

Name of polymerforms Examples of polymer forms

Amino acids Amino acidsProteins (also called 

polypeptides)Fibrous proteins andglobular 

proteins

Carbohydrates Monosaccharides Polysaccharides Starch, glycogenand cellulose

Nucleic acids Nucleotides Polynucleotides DNA and RNA

Amino acids and proteins[edit]Proteins are made of amino acids arranged in a linear chain joined together by peptide bonds. Many proteins are enzymesthat catalyze the chemical reactions in metabolism. Other proteins have structural or mechanical functions, such as those that form the cytoskeleton, a system of scaffolding that maintains the cell shape.[6] Proteins are also important in cell signaling, immune responses, cell adhesion, active transport across membranes, and the cell cycle.[7] Amino acids also contribute to cellular energy metabolism by providing a carbon source for entry into the citric acid cycle (tricarboxylic acid cycle),[8] especially when a primary source of energy, such as glucose, is scarce, or when cells undergo metabolic stress.[9]

Lipids[edit]Lipids are the most diverse group of biochemicals. Their main structural uses are as part of biological membranes both internal and external, such as the cell membrane, or as a source of

energy.[7] Lipids are usually defined as hydrophobic oramphipathic biological molecules but will dissolve in organic solvents such as benzene or chloroform.[10] The fats are a large group of compounds that contain fatty acids and glycerol; a glycerol molecule attached to three fatty acid esters is called atriacylglyceride.[11] Several variations on this basic structure exist, including alternate backbones such as sphingosine in thesphingolipids, and hydrophilic groups such as phosphate as in phospholipids. Steroids such as cholesterol are another major class of lipids.[12]

Carbohydrates[edit]

Glucose can exist in both a straight-chain and ring form.

Carbohydrates are aldehydes or ketones, with many hydroxyl groups attached, that can exist as straight chains or rings. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport ofenergy (starch, glycogen) and structural components (cellulose in plants, chitin in animals).[7] The basic carbohydrate units are called monosaccharides and includegalactose, fructose, and most importantly glucose. Monosaccharides can be linked together to form polysaccharides in almost limitless ways.[13]

Nucleotides[edit]The two nucleic acids, DNA and RNA, are polymers of nucleotides. Each nucleotide is composed of a phosphate attached to a ribose or deoxyribose sugar group which is attached to a nitrogenous base. Nucleic acids are critical for the storage and use of genetic information, and its interpretation through the processes of transcription and protein biosynthesis.[7] This information is protected by DNA repair mechanisms and propagated through DNA replication. Manyviruses have an RNA genome, such as HIV, which uses reverse transcription to create a DNA template from its viral RNA genome.[14] RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can catalyze chemical reactions. Individual nucleosides are made by attaching a nucleobase to a ribose sugar. These bases are heterocyclic rings containing nitrogen, classified as purines or pyrimidines. Nucleotides also act as coenzymes in metabolic-group-transfer reactions.[15]

Coenzymes[edit]

Structure of the coenzyme acetyl-CoA.The transferable acetyl group is bonded to the sulfur atom at the

extreme left.

Main article: Coenzyme

Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer offunctional groups of atoms and their bonds within molecules.[16] This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions.[15]These group-transfer intermediates are called coenzymes. Each class of group-transfer reactions is carried out by a particular coenzyme, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. These coenzymes are therefore continuously made, consumed and then recycled.[17]

One central coenzyme is adenosine triphosphate (ATP), the universal energy currency of cells. This nucleotide is used to transfer chemical energy between different chemical reactions. There is only a small amount of ATP in cells, but as it is continuously regenerated, the human body can use about its own weight in ATP per day.[17] ATP acts as a bridge betweencatabolism and anabolism. Catabolism breaks down molecules and anabolism puts them together. Catabolic reactions generate ATP and anabolic reactions consume it. It also serves as a carrier of phosphate groups in phosphorylationreactions.

A vitamin is an organic compound needed in small quantities that cannot be made in cells. In human nutrition, most vitamins function as coenzymes after modification; for example, all water-soluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells.[18] Nicotinamide adenine dinucleotide (NAD+), a derivative of vitamin B3 (niacin), is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of dehydrogenases remove electrons from their substrates and reduce NAD+ into NADH. This reduced form of the coenzyme is then a substrate for any of thereductases in the cell that need to reduce their substrates.[19] Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD+/NADH form is more important in catabolic reactions, while NADP+/NADPH is used in anabolic reactions.

Structure of hemoglobin. The protein subunits are in red and blue, and the iron-containing heme groups in

green. From PDB: 1GZX.

Minerals and cofactors[edit]Further information: Metal Ions in Life Sciences, Metal metabolism, andbioinorganic chemistry

Inorganic elements play critical roles in metabolism; some are abundant (e.g. sodium and potassium) while others function at minute concentrations. About 99% of a mammal's mass is made up of the elements carbon, nitrogen, calcium, sodium, chlorine, potassium,hydrogen, phosphorus, oxygen and sulfur.[20] Organic compounds(proteins, lipids and carbohydrates) contain the majority of the carbon and nitrogen; most of the oxygen and hydrogen is present as water.[20]

The abundant inorganic elements act as ionic electrolytes. The most important ions are sodium, potassium, calcium, magnesium, chloride,phosphate and the organic ion bicarbonate. The maintenance of precise ion gradients across cell membranes maintains osmotic pressure and pH.[21] Ions are also critical for nerve and muscle function, as action potentials in these tissues are produced by the exchange of electrolytes between the extracellular fluid and the cell's fluid, thecytosol.[22] Electrolytes enter and leave cells through proteins in the cell membrane called ion channels. For example,muscle contraction depends upon the movement of calcium, sodium and potassium through ion channels in the cell membrane and T-tubules.[23]

Transition metals are usually present as trace elements in organisms, with zinc and iron being most abundant of those.[24][25]These metals are used in some proteins as cofactors and are essential for the activity of enzymes such as catalase and oxygen-carrier proteins such as hemoglobin.[26] Metal cofactors are bound tightly to specific sites in proteins; although enzyme cofactors can be modified during catalysis, they always return to their original state by the end of the reaction catalyzed. Metal micronutrients are taken up into organisms by specific transporters and bind to storage proteins such asferritin or metallothionein when not in use.[27][28]

Catabolism[edit]

Catabolism is the set of metabolic processes that break down large molecules. These include breaking down and oxidizing food molecules. The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions. The exact nature of these catabolic reactions differ from organism to organism and organisms can be classified based on their sources of energy and carbon (their primary nutritional groups), as shown in the table below. Organic molecules are used as a source of energy by organotrophs, while lithotrophs use inorganic substrates and phototrophscapture sunlight as chemical energy. However, all these different forms of metabolism depend on redox reactions that involve the transfer of electrons from reduced donor molecules such as organic molecules, water, ammonia, hydrogen sulfide or ferrous ions to acceptor molecules such as oxygen, nitrate or sulfate.[29] In animals these reactions involve complex organic molecules that are broken down to simpler molecules, such as carbon dioxide and water. In photosyntheticorganisms such as plants and cyanobacteria, these electron-transfer reactions do not release energy, but are used as a way of storing energy absorbed from sunlight.[30]

Classification of organisms based on their metabolism

Energy source

sunlightphoto-

-troph

Preformed 

molecule

chemo-

s

Electron 

donor

organic compou

nd

organo-

inorganic compou

ndlitho-

Carbon 

source

organic compou

nd

hetero-

inorganic compou

ndauto-

The most common set of catabolic reactions in animals can be separated into three main stages. In the first, large organic molecules such as proteins, polysaccharides or lipids are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to yet smaller molecules, usually acetyl coenzyme A (acetyl-CoA), which releases some energy. Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the citric acid cycle and electron transport chain, releasing the energy that is stored by reducing the coenzyme nicotinamide adenine dinucleotide (NAD+) into NADH.

Digestion[edit]Further information: Digestion and gastrointestinal tract

Macromolecules such as starch, cellulose or proteins cannot be rapidly taken up by cells and must be broken into their smaller units before they can be used in cell metabolism. Several common classes of enzymes digest these polymers. These digestive enzymes include proteases that digest proteins into amino acids, as well as glycoside hydrolases that digest polysaccharides into simple sugars known as monosaccharides.

Microbes simply secrete digestive enzymes into their surroundings,[31][32] while animals only secrete these enzymes from specialized cells in their guts.[33] The amino acids or sugars released by these extracellular enzymes are then pumped into cells by active transport proteins.[34][35]

A simplified outline of the catabolism of proteins,carbohydrates and fats

Energy from organic compounds[edit]Further information: Cellular respiration, fermentation, carbohydrate catabolism, fat catabolism and protein catabolism

Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Carbohydrates are usually taken into cells once they have been digested into monosaccharides.[36] Once inside, the major route of breakdown is glycolysis, where sugars such as glucose andfructose are converted into pyruvate and some ATP is generated.[37]Pyruvate is an intermediate in several metabolic pathways, but the majority is converted to acetyl-CoA and fed into the citric acid cycle. Although some more ATP is generated in the citric acid cycle, the most important product is NADH, which is made from NAD+ as the acetyl-CoA is oxidized. This oxidation releases carbon dioxide as a waste product. In anaerobic conditions, glycolysis produces lactate, through the enzyme lactate dehydrogenase re-oxidizing NADH to NAD+ for re-use in glycolysis. An alternative route for glucose breakdown is the pentose phosphate pathway, which reduces the coenzymeNADPH and produces pentose sugars such as ribose, the sugar component of nucleic acids.

Fats are catabolised by hydrolysis to free fatty acids and glycerol. The glycerol enters glycolysis and the fatty acids are broken down by beta oxidation to release acetyl-CoA, which then is fed into the citric acid cycle. Fatty acids release more energy upon oxidation than carbohydrates because carbohydrates contain more oxygen in their structures. Steroids are also broken down by some bacteria in a process similar to beta oxidation, and this breakdown process involves the release of significant amounts of acetyl-CoA, propionyl-CoA, and pyruvate, which can all be used by the cell for energy. M. tuberculosis can also grow on the lipid cholesterol as a sole source of carbon, and genes involved in the cholesterol use pathway(s) have been validated as important during various stages of the infection lifecycle of M. tuberculosis.[38]

Amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and carbon dioxide as a source of energy.[39] The oxidation pathway starts with the removal of the amino group by a transaminase. The amino group is fed into the urea cycle, leaving a deaminated carbon skeleton in the form of a keto acid. Several of these keto acids are intermediates in the citric acid cycle, for example the deamination of glutamate forms α-ketoglutarate.[40] The glucogenic amino acids can also be converted into glucose, through gluconeogenesis (discussed below).[41]

Energy transformations[edit]

Oxidative phosphorylation[edit]Further information: Oxidative phosphorylation, chemiosmosis and mitochondrion

In oxidative phosphorylation, the electrons removed from organic molecules in areas such as the protagon acid cycle are transferred to oxygen and the energy released is used to make ATP. This is done in eukaryotes by a series of proteins in the membranes of mitochondria called the electron transport chain. In prokaryotes, these proteins are found in the cell'sinner membrane.[42] These proteins use the energy released from passing electrons from reduced molecules like NADH ontooxygen to pump protons across a membrane.[43]

Mechanism of ATP synthase. ATP is shown in red, ADP and phosphate in pink and the rotating stalk subunit in

black.

Pumping protons out of the mitochondria creates a proton concentration differenceacross the membrane and generates an electrochemical gradient.[44] This force drives protons back into the mitochondrion through the base of an enzyme calledATP synthase. The flow of protons makes the stalk subunit rotate, causing the active site of the synthase domain to change shape and phosphorylate adenosine diphosphate – turning it into ATP.[17]

Energy from inorganic compounds[edit]Further information: Microbial metabolism and nitrogen cycle

Chemolithotrophy is a type of metabolism found in prokaryotes where energy is obtained from the oxidation of inorganic compounds. These organisms can usehydrogen,[45] reduced sulfur compounds (such as sulfide, hydrogen sulfide andthiosulfate),[1] ferrous iron (FeII) [46]  or ammonia [47]  as sources of reducing power and they gain energy from the oxidation of these compounds with electron acceptors such as oxygen or nitrite.[48] These microbial processes are important in global biogeochemical cycles such asacetogenesis, nitrification and denitrification and are critical for soil fertility.[49][50]

Energy from light[edit]Further information: Phototroph, photophosphorylation, chloroplast

The energy in sunlight is captured by plants, cyanobacteria, purple bacteria, green sulfur bacteria and some protists. This process is often coupled to the conversion of carbon dioxide into organic compounds, as part of photosynthesis, which is discussed below. The energy capture and carbon fixation systems can however operate separately in prokaryotes, as purple bacteria and green sulfur bacteria can use sunlight as a source of energy, while switching between carbon fixation and the fermentation of organic compounds.[51][52]

In many organisms the capture of solar energy is similar in principle to oxidative phosphorylation, as it involves the storage of energy as a proton concentration gradient. This proton motive force then drives ATP synthesis.[17] The electrons needed to drive this electron transport chain come from light-gathering proteins called photosynthetic reaction centres orrhodopsins. Reaction centers are classed into two types depending on the type of photosynthetic pigment present, with most photosynthetic bacteria only having one type, while plants and cyanobacteria have two. [53]

In plants, algae, and cyanobacteria, photosystem II uses light energy to remove electrons from water, releasing oxygen as a waste product. The electrons then flow to the cytochrome b6f complex, which uses their energy to pump protons across thethylakoid membrane in the chloroplast.[30] These protons move back through the membrane as they drive the ATP synthase, as before. The electrons then flow through photosystem I and can then either be used to reduce the coenzyme NADP+, for use in the Calvin cycle, which is discussed below, or recycled for further ATP generation.[54]

Anabolism[edit]Further information: Anabolism

Anabolism is the set of constructive metabolic processes where the energy released by catabolism is used to synthesize complex molecules. In general, the complex molecules that make up cellular structures are constructed step-by-step from small and simple precursors. Anabolism involves three basic stages. First, the production of precursors such as amino acids, monosaccharides, isoprenoids and nucleotides, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as proteins, polysaccharides, lipids and nucleic acids.

Organisms differ in how many of the molecules in their cells they can construct for themselves. Autotrophs such as plants can construct the complex organic molecules in cells such as polysaccharides and proteins from simple molecules likecarbon dioxide and water. Heterotrophs, on the other hand, require a source of more complex substances, such as monosaccharides and amino acids, to produce these complex molecules. Organisms can be further classified by ultimate source of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation reactions.

Carbon fixation[edit]Further information: Photosynthesis, carbon fixation and chemosynthesis

Plant cells (bounded by purple walls) filled with chloroplasts (green), which are the site of photosynthesis

Photosynthesis is the synthesis of carbohydrates from sunlight and carbon dioxide(CO2). In plants, cyanobacteria and algae, oxygenic photosynthesis splits water, with oxygen produced as a waste product. This process uses the ATP and NADPH produced by the photosynthetic reaction centres, as described above, to convert CO2 into glycerate 3-phosphate, which can then be converted into

glucose. This carbon-fixation reaction is carried out by the enzyme RuBisCO as part of theCalvin   – Benson cycle.[55] Three types of photosynthesis occur in plants, C3 carbon fixation, C4 carbon fixation and CAM photosynthesis. These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO2 directly, while C4 and CAM photosynthesis incorporate the CO2 into other compounds first, as adaptations to deal with intense sunlight and dry conditions. [56]

In photosynthetic prokaryotes the mechanisms of carbon fixation are more diverse. Here, carbon dioxide can be fixed by the Calvin – Benson cycle, a reversed citric acid cycle,[57] or the carboxylation of acetyl-CoA.[58][59] Prokaryotic chemoautotrophs also fix CO2 through the Calvin – Benson cycle, but use energy from inorganic compounds to drive the reaction.[60]

Carbohydrates and glycans[edit]Further information: Gluconeogenesis, glyoxylate cycle, glycogenesis and glycosylation

In carbohydrate anabolism, simple organic acids can be converted into monosaccharides such as glucose and then used to assemble polysaccharides such as starch. The generation of glucose from compounds like pyruvate, lactate, glycerol,glycerate 3-phosphate and amino acids is called gluconeogenesis. Gluconeogenesis converts pyruvate to glucose-6-phosphate through a series of intermediates, many of which are shared with glycolysis.[37] However, this pathway is not simply glycolysis run in reverse, as several steps are catalyzed by non-glycolytic enzymes. This is important as it allows the formation and breakdown of glucose to be regulated separately, and prevents both pathways from running simultaneously in a futile cycle.[61][62]

Although fat is a common way of storing energy, in vertebrates such as humans the fatty acids in these stores cannot be converted to glucose through gluconeogenesis as these organisms cannot convert acetyl-CoA into pyruvate; plants do, but animals do not, have the necessary enzymatic machinery.[63] As a result, after long-term starvation, vertebrates need to produce ketone bodies from fatty acids to replace glucose in tissues such as the brain that cannot metabolize fatty acids. [64]In other organisms such as plants and bacteria, this metabolic problem is solved using the glyoxylate cycle, which bypasses the decarboxylation step in the citric acid cycle and allows the transformation of acetyl-CoA to oxaloacetate, where it can be used for the production of glucose.[63][65]

Polysaccharides and glycans are made by the sequential addition of monosaccharides by glycosyltransferase from a reactive sugar-phosphate donor such as uridine diphosphate glucose (UDP-glucose) to an acceptor hydroxyl group on the growing polysaccharide. As any of the hydroxyl groups on the ring of the substrate can be acceptors, the polysaccharides produced can have straight or branched structures.[66] The polysaccharides produced can have structural or metabolic functions themselves, or be transferred to lipids and proteins by enzymes called oligosaccharyltransferases.[67][68]

Fatty acids, isoprenoids and steroids[edit]Further information: Fatty acid synthesis, steroid metabolism

Simplified version of the steroid synthesis pathway with the intermediates isopentenyl

pyrophosphate (IPP), dimethylallyl pyrophosphate (DMAPP), geranyl pyrophosphate (GPP)

andsqualene shown. Some intermediates are omitted for clarity.

Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl-CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the acyl group, reduce it to an alcohol, dehydrate it to an alkene group and then reduce it again to an alkane group. The enzymes of fatty acid biosynthesis are divided into two groups: in animals and fungi, all these fatty acid synthase reactions are carried out by a single multifunctional type I protein,[69] while in plantplastids and bacteria separate type II enzymes perform each step in the pathway. [70][71]

Terpenes and isoprenoids are a large class of lipids that include the carotenoids and form the largest class of plantnatural products.[72] These compounds are made by the assembly and modification of isoprene units donated from the reactive precursors isopentenyl pyrophosphate anddimethylallyl pyrophosphate.[73] These precursors can be made in different ways. In animals and archaea, the mevalonate pathway produces these compounds from acetyl-CoA,[74] while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates.[73][75]One important reaction that uses these activated isoprene donors is steroid biosynthesis. Here, the isoprene units are joined together to make squalene and then folded up and formed into a set of rings to make lanosterol.[76] Lanosterol can then be converted into other steroids such as cholesteroland ergosterol.[76][77]

Proteins[edit]Further information: Protein biosynthesis, amino acid synthesis

Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants can synthesize all twenty, but mammals can only synthesize eleven nonessential amino acids, so nine essential amino acids must be obtained from food.[7] Some simple parasites, such as the

bacteria Mycoplasma pneumoniae, lack all amino acid synthesis and take their amino acids directly from their hosts.[78] All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and glutamine. Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then transaminated to form an amino acid.[79]

Amino acids are made into proteins by being joined together in a chain of peptide bonds. Each different protein has a unique sequence of amino acid residues: this is its primary structure. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a transfer RNA molecule through an esterbond. This aminoacyl-tRNA precursor is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase.[80] This aminoacyl-tRNA is then a substrate for the ribosome, which joins the amino acid onto the elongating protein chain, using the sequence information in a messenger RNA.[81]

Nucleotide synthesis and salvage[edit]Further information: Nucleotide salvage, pyrimidine biosynthesis, and purine metabolism

Nucleotides are made from amino acids, carbon dioxide and formic acid in pathways that require large amounts of metabolic energy.[82] Consequently, most organisms have efficient systems to salvage preformed nucleotides.[82][83] Purines are synthesized as nucleosides (bases attached to ribose).[84] Both adenine and guanine are made from the precursor nucleoside inosine monophosphate, which is synthesized using atoms from the amino acids glycine, glutamine, and aspartic acid, as well as formate transferred from the coenzyme tetrahydrofolate. Pyrimidines, on the other hand, are synthesized from the base orotate, which is formed from glutamine and aspartate.[85]

Xenobiotics and redox metabolism[edit]Further information: Xenobiotic metabolism, drug metabolism, Alcohol metabolism and antioxidants

All organisms are constantly exposed to compounds that they cannot use as foods and would be harmful if they accumulated in cells, as they have no metabolic function. These potentially damaging compounds are called xenobiotics.[86]Xenobiotics such as synthetic drugs, natural poisons and antibiotics are detoxified by a set of xenobiotic-metabolizing enzymes. In humans, these include cytochrome P450 oxidases,[87] UDP-glucuronosyltransferases,[88] and glutathione   S - transferases.[89] This system of enzymes acts in three stages to firstly oxidize the xenobiotic (phase I) and then conjugate water-soluble groups onto the molecule (phase II). The modified water-soluble xenobiotic can then be pumped out of cells and in multicellular organisms may be further metabolized before being excreted (phase III). In ecology, these reactions are particularly important in microbial biodegradation of pollutants and the bioremediation of contaminated land and oil spills.[90]Many of these microbial reactions are shared with multicellular organisms, but due to the incredible diversity of types of microbes these organisms are able to deal with a far wider range of xenobiotics than multicellular organisms, and can degrade even persistent organic pollutants such as organochloride compounds.[91]

A related problem for aerobic organisms is oxidative stress.[92] Here, processes including oxidative phosphorylation and the formation of disulfide bonds during protein folding produce reactive oxygen species such as hydrogen peroxide.[93] These damaging oxidants are removed by antioxidant metabolites such as glutathione and enzymes such as catalases andperoxidases.[94][95]

Thermodynamics of living organisms[edit]Further information: Biological thermodynamics

Living organisms must obey the laws of thermodynamics, which describe the transfer of heat and work. The second law of thermodynamics states that in any closed system, the amount of entropy (disorder) cannot decrease. Although living organisms' amazing complexity appears to contradict this law, life is possible as all organisms are open systems that exchange matter and energy with their surroundings. Thus living systems are not in equilibrium, but instead are dissipative systems that maintain their state of high complexity by causing a larger increase in the entropy of their environments.[96] The metabolism of a cell achieves this by coupling the spontaneous processes of catabolism to the non-spontaneous processes of anabolism. In thermodynamic terms, metabolism maintains order by creating disorder.[97]

Regulation and control[edit]Further information: Metabolic pathway, metabolic control analysis, hormone, regulatory enzymes, and cell signaling

As the environments of most organisms are constantly changing, the reactions of metabolism must be finely regulated to maintain a constant set of conditions within cells, a condition called homeostasis.[98][99] Metabolic regulation also allows organisms to respond to signals and interact actively with their environments.[100] Two closely linked concepts are important for understanding how metabolic pathways are controlled. Firstly, the regulation of an enzyme in a pathway is how its activity is increased and decreased in response to signals. Secondly, the control exerted by this enzyme is the effect that these changes in its activity have on the overall rate of the pathway (the flux through the pathway).[101] For example, an enzyme may show large changes in activity (i.e. it is highly regulated) but if these changes have little effect on the flux of a metabolic pathway, then this enzyme is not involved in the control of the pathway. [102]

Effect of insulin on glucose uptake and metabolism. Insulin binds to its receptor (1), which in turn starts

many protein activation cascades (2). These include: translocation of Glut-4 transporter to the plasma

membrane and influx of glucose (3),glycogen synthesis (4), glycolysis (5) and fatty acidsynthesis (6).

There are multiple levels of metabolic regulation. In intrinsic regulation, the metabolic pathway self-regulates to respond to changes in the levels of substrates or products; for example, a decrease in the amount of product can increase the flux through the pathway to compensate.[101] This type of regulation often involves allosteric regulation of the activities of multiple enzymes in the pathway.[103]Extrinsic control involves a cell in a multicellular organism changing its metabolism in response to signals from other cells. These signals are usually in the form of soluble messengers such as hormones andgrowth factors and are detected by specific receptors on the cell surface.[104] These signals are then transmitted inside the cell bysecond messenger systems that often involved the phosphorylation of proteins.[105]

A very well understood example of extrinsic control is the regulation of glucose metabolism by the hormone insulin.[106] Insulin is produced in response to rises in blood glucose levels. Binding of the

hormone to insulin receptors on cells then activates a cascade ofprotein kinases that cause the cells to take up glucose and convert it into storage molecules such as fatty acids andglycogen.[107] The metabolism of glycogen is controlled by activity of phosphorylase, the enzyme that breaks down glycogen, and glycogen synthase, the enzyme that makes it. These enzymes are regulated in a reciprocal fashion, with phosphorylation inhibiting glycogen synthase, but activating phosphorylase. Insulin causes glycogen synthesis by activatingprotein phosphatases and producing a decrease in the phosphorylation of these enzymes.[108]

Evolution[edit]Further information: Molecular evolution and phylogenetics

Evolutionary tree showing the common ancestry of organisms from all three domains of life. Bacteria are

colored blue, eukaryotes red, andarchaea green. Relative positions of some of the phyla included are shown

around the tree.

The central pathways of metabolism described above, such as glycolysis and the citric acid cycle, are present in all three domains of living things and were present in the last universal ancestor.[3]

[109] This universal ancestral cell was prokaryotic and probably amethanogen that had extensive amino acid, nucleotide, carbohydrate and lipid metabolism.[110][111] The retention of these ancient pathways during laterevolution may be the result of these reactions having been an optimal solution to their particular metabolic problems, with pathways such as glycolysis and the citric acid cycle producing their end products highly efficiently and in a minimal number of steps.[4][5]Mutation changes that affect non-coding DNA segments may merely affect the metabolic efficiency of the individual for whom the mutation occurs.[112] The first pathways of enzyme-based metabolism may have been parts of purine nucleotide metabolism, while previous metabolic pathways were a part of the ancient RNA world.[113]

Many models have been proposed to describe the mechanisms by which novel metabolic pathways evolve. These include the sequential addition of novel enzymes to a short ancestral pathway, the duplication and then divergence of entire pathways as well as the recruitment of pre-existing enzymes and their assembly into a novel reaction pathway.[114] The relative importance of these mechanisms is unclear, but genomic studies have shown that enzymes in a pathway are likely to have a shared ancestry, suggesting that many pathways have evolved in a step-by-step fashion with

novel functions created from pre-existing steps in the pathway.[115] An alternative model comes from studies that trace the evolution of proteins' structures in metabolic networks, this has suggested that enzymes are pervasively recruited, borrowing enzymes to perform similar functions in different metabolic pathways (evident in the MANET database)[116] These recruitment processes result in an evolutionary enzymatic mosaic.[117] A third possibility is that some parts of metabolism might exist as "modules" that can be reused in different pathways and perform similar functions on different molecules.[118]

As well as the evolution of new metabolic pathways, evolution can also cause the loss of metabolic functions. For example, in some parasites metabolic processes that are not essential for survival are lost and preformed amino acids, nucleotides and carbohydrates may instead be scavenged from the host.[119] Similar reduced metabolic capabilities are seen inendosymbiotic organisms.[120]

Investigation and manipulation[edit]Further information: Protein methods, proteomics, metabolomics and metabolic network modelling

Metabolic network of the Arabidopsis thaliana citric acid cycle. Enzymes and metabolites are shown as red

squares and the interactions between them as black lines.

Classically, metabolism is studied by a reductionist approach that focuses on a single metabolic pathway. Particularly valuable is the use of radioactive tracers at the whole-organism, tissue and cellular levels, which define the paths from precursors to final products by identifying radioactively labelled intermediates and products.[121] The enzymes that catalyze these chemical reactions can then be purified and their kineticsand responses to inhibitors investigated. A parallel approach is to identify the small molecules in a cell or tissue; the complete set of these molecules is called the metabolome. Overall, these studies give a good view of the structure and function of simple metabolic pathways, but are inadequate when applied to more complex systems such as the metabolism of a complete cell.[122]

An idea of the complexity of the metabolic networks in cells that contain thousands of different enzymes is given by the figure showing the interactions between just 43 proteins and 40 metabolites to the right: the sequences of genomes provide lists containing anything up to 45,000 genes.

[123] However, it is now possible to use this genomic data to reconstruct complete networks of biochemical reactions and produce more holistic mathematical models that may explain and predict their behavior.[124] These models are especially powerful when used to integrate the pathway and metabolite data obtained through classical methods with data on gene expression from proteomicand DNA microarray studies.[125] Using these techniques, a model of human metabolism has now been produced, which will guide future drug discovery and biochemical research.[126] These models are now used in network analysis, to classify human diseases into groups that share common proteins or metabolites.[127][128]

Bacterial metabolic networks are a striking example of bow-tie [129] [130] [131]  organization, an architecture able to input a wide range of nutrients and produce a large variety of products and complex macromolecules using a relatively few intermediate common currencies.

A major technological application of this information is metabolic engineering. Here, organisms such as yeast, plants orbacteria are genetically modified to make them more useful in biotechnology and aid the production of drugs such asantibiotics or industrial chemicals such as 1,3-propanediol and shikimic acid.[132] These genetic modifications usually aim to reduce the amount of energy used to produce the product, increase yields and reduce the production of wastes. [133]

History[edit]Further information: History of biochemistry and history of molecular biology

Santorio Santorio in his steelyard balance, fromArs de statica medicina, first published 1614

The term metabolism is derived from the Greek Μεταβολισμός – "Metabolismos" for "change", or "overthrow".[134] The first documented references of metabolism were made by Ibn al-Nafis in his 1260 AD work titled Al-Risalah al-Kamiliyyah fil Siera al-Nabawiyyah (The Treatise of Kamil on the Prophet's Biography) which included the following phrase "Both the body and its parts are in a continuous state of dissolution and nourishment, so they are inevitably undergoing permanent change."[135] The history of the scientific study of metabolism spans several centuries and has moved from examining whole animals in early studies, to examining individual metabolic reactions in modern biochemistry. The first controlled experiments in human metabolism were published by Santorio Santorio in 1614 in his book Ars de statica medicina.[136] He described how he weighed himself before and after eating, sleep, working, sex, fasting, drinking, and excreting. He found that most of the food he took in was lost through what he called "insensible perspiration".

In these early studies, the mechanisms of these metabolic processes had not been identified and a vital force was thought to animate living tissue.[137] In the 19th century, when studying

thefermentation of sugar to alcohol by yeast, Louis Pasteur concluded that fermentation was catalyzed by substances within the yeast cells he called "ferments". He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells."[138] This discovery, along with the publication by Friedrich Wöhler in 1828 of a paper on the chemical synthesis ofurea,[139] and is notable for being the first organic compound prepared from wholly inorganic precursors. This proved that the organic compounds and chemical reactions found in cells were no different in principle than any other part of chemistry.

It was the discovery of enzymes at the beginning of the 20th century by Eduard Buchner that separated the study of the chemical reactions of metabolism from the biological study of cells, and marked the beginnings of biochemistry.[140] The mass of biochemical knowledge grew rapidly throughout the early 20th century. One of the most prolific of these modern biochemists was Hans Krebs who made huge contributions to the study of metabolism.[141] He discovered the urea cycle and later, working with Hans Kornberg, the citric acid cycle and the glyoxylate cycle.[142][65] Modern biochemical research has been greatly aided by the development of new techniques such as chromatography, X-ray diffraction, NMR spectroscopy,radioisotopic labelling, electron microscopy and molecular dynamics simulations. These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells.

MetabolismFrom Wikipedia, the free encyclopedia

"Cell metabolism" redirects here. For the journal, see Cell Metabolism.

For the architectural movement, see Metabolism (architecture).

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Structure of adenosine triphosphate(ATP), a central intermediate in energy metabolism

Metabolism (from Greek: μεταβολή metabolē, "change") is the set of life-sustaining chemical transformations within the cells of living organisms. Theseenzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to all chemical reactions that occur in living organisms, includingdigestion and the transport of substances into and between different cells, in which case the set of reactions within the cells is called intermediary metabolism or intermediate metabolism.

Metabolism is usually divided into two categories: catabolism, the breaking down of organic matter by way of cellular respiration, and anabolism, thebuilding up of components of cells such as proteins and nucleic acids. Usually, breaking down releases energy and building up consumes energy.

The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energythat will not occur by themselves, by coupling them to spontaneous reactionsthat release energy. Enzymes act as catalysts that allow the reactions to proceed more rapidly. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or to signals from other cells.

The metabolic system of a particular organism determines which substances it will find nutritious and which poisonous. For example, some prokaryotes usehydrogen sulfide as a nutrient, yet this gas is poisonous to animals.[1] The speed of metabolism, the metabolic rate, influences how much food an organism will require, and also affects how it is able to obtain that food.

A striking feature of metabolism is the similarity of the basic metabolic pathways and components between even vastly different species.[2] For example, the set ofcarboxylic acids that are best known as the intermediates in the citric acid cycle are present in all known organisms, being found in species as diverse as the unicellularbacterium Escherichia coli and huge multicellular organisms like elephants.[3] These striking similarities in metabolic pathways are likely due to their early appearance inevolutionary history, and their retention because of their efficacy.[4][5]

Contents  [hide] 

1 Key biochemicals o 1.1 Amino acids and proteins o 1.2 Lipids o 1.3 Carbohydrates o 1.4 Nucleotides o 1.5 Coenzymes o 1.6 Minerals and cofactors

2 Catabolism o 2.1 Digestion o 2.2 Energy from organic compounds

3 Energy transformations o 3.1 Oxidative phosphorylation o 3.2 Energy from inorganic compounds o 3.3 Energy from light

4 Anabolism o 4.1 Carbon fixation o 4.2 Carbohydrates and glycans o 4.3 Fatty acids, isoprenoids and steroids o 4.4 Proteins o 4.5 Nucleotide synthesis and salvage

5 Xenobiotics and redox metabolism 6 Thermodynamics of living organisms 7 Regulation and control 8 Evolution

9 Investigation and manipulation 10 History 11 See also 12 References 13 Further reading 14 External links

Key biochemicals[edit]Further information: Biomolecule, cell (biology) and biochemistry

Structure of a triacylglycerol lipid

Most of the structures that make up animals, plants and microbes are made from three basic classes of molecule: amino acids, carbohydrates and lipids(often called fats). As these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or by breaking them down and using them as a source of energy, by their digestion. These biochemicals can be joined together to make polymerssuch as DNA and proteins, essential macromolecules of life.

Type of molecule

Name ofmonomer forms

Name of polymerforms Examples of polymer forms

Amino acids Amino acidsProteins (also called 

polypeptides)Fibrous proteins andglobular 

proteins

Carbohydrates Monosaccharides Polysaccharides Starch, glycogenand cellulose

Nucleic acids Nucleotides Polynucleotides DNA and RNA

Amino acids and proteins[edit]

Proteins are made of amino acids arranged in a linear chain joined together by peptide bonds. Many proteins are enzymesthat catalyze the chemical reactions in metabolism. Other proteins have structural or mechanical functions, such as those that form the cytoskeleton, a system of scaffolding that maintains the cell shape.[6] Proteins are also important in cell signaling, immune responses, cell adhesion, active transport across membranes, and the cell cycle.[7] Amino acids also contribute to cellular energy metabolism by providing a carbon source for entry into the citric acid cycle (tricarboxylic acid cycle),[8] especially when a primary source of energy, such as glucose, is scarce, or when cells undergo metabolic stress.[9]

Lipids[edit]Lipids are the most diverse group of biochemicals. Their main structural uses are as part of biological membranes both internal and external, such as the cell membrane, or as a source of energy.[7] Lipids are usually defined as hydrophobic oramphipathic biological molecules but will dissolve in organic solvents such as benzene or chloroform.[10] The fats are a large group of compounds that contain fatty acids and glycerol; a glycerol molecule attached to three fatty acid esters is called atriacylglyceride.[11] Several variations on this basic structure exist, including alternate backbones such as sphingosine in thesphingolipids, and hydrophilic groups such as phosphate as in phospholipids. Steroids such as cholesterol are another major class of lipids.[12]

Carbohydrates[edit]

Glucose can exist in both a straight-chain and ring form.

Carbohydrates are aldehydes or ketones, with many hydroxyl groups attached, that can exist as straight chains or rings. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport ofenergy (starch, glycogen) and structural components (cellulose in plants, chitin in animals).[7] The basic carbohydrate units are called monosaccharides and includegalactose, fructose, and most importantly glucose. Monosaccharides can be linked together to form polysaccharides in almost limitless ways.[13]

Nucleotides[edit]The two nucleic acids, DNA and RNA, are polymers of nucleotides. Each nucleotide is composed of a phosphate attached to a ribose or deoxyribose sugar group which is attached to a nitrogenous base. Nucleic acids are critical for the storage and use of genetic information, and its interpretation through the processes of transcription and protein biosynthesis.[7] This information is protected by DNA repair mechanisms and propagated through DNA replication. Manyviruses have an RNA genome, such as HIV, which uses reverse transcription to create a DNA template from its viral RNA genome.[14] RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can catalyze chemical reactions. Individual nucleosides are made by attaching a nucleobase to a ribose sugar. These bases are heterocyclic rings containing nitrogen, classified as purines or pyrimidines. Nucleotides also act as coenzymes in metabolic-group-transfer reactions.[15]

Coenzymes[edit]

Structure of the coenzyme acetyl-CoA.The transferable acetyl group is bonded to the sulfur atom at the

extreme left.

Main article: Coenzyme

Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer offunctional groups of atoms and their bonds within molecules.[16] This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions.[15]These group-transfer intermediates are called coenzymes. Each class of group-transfer reactions is carried out by a particular coenzyme, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. These coenzymes are therefore continuously made, consumed and then recycled.[17]

One central coenzyme is adenosine triphosphate (ATP), the universal energy currency of cells. This nucleotide is used to transfer chemical energy between different chemical reactions. There is only a small amount of ATP in cells, but as it is continuously regenerated, the human body can use about its own weight in ATP per day.[17] ATP acts as a bridge betweencatabolism and anabolism. Catabolism breaks down molecules and anabolism puts them together. Catabolic reactions generate ATP and anabolic reactions consume it. It also serves as a carrier of phosphate groups in phosphorylationreactions.

A vitamin is an organic compound needed in small quantities that cannot be made in cells. In human nutrition, most vitamins function as coenzymes after modification; for example, all water-soluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells.[18] Nicotinamide adenine dinucleotide (NAD+), a derivative of vitamin B3 (niacin), is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of dehydrogenases remove electrons from their substrates and reduce NAD+ into NADH. This reduced form of the coenzyme is then a substrate for any of thereductases in the cell that need to reduce their substrates.[19] Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD+/NADH form is more important in catabolic reactions, while NADP+/NADPH is used in anabolic reactions.

Structure of hemoglobin. The protein subunits are in red and blue, and the iron-containing heme groups in

green. From PDB: 1GZX.

Minerals and cofactors[edit]Further information: Metal Ions in Life Sciences, Metal metabolism, andbioinorganic chemistry

Inorganic elements play critical roles in metabolism; some are abundant (e.g. sodium and potassium) while others function at minute concentrations. About 99% of a mammal's mass is made up of the elements carbon, nitrogen, calcium, sodium, chlorine, potassium,hydrogen, phosphorus, oxygen and sulfur.[20] Organic compounds(proteins, lipids and carbohydrates) contain the majority of the carbon and nitrogen; most of the oxygen and hydrogen is present as water.[20]

The abundant inorganic elements act as ionic electrolytes. The most important ions are sodium, potassium, calcium, magnesium, chloride,phosphate and the organic ion bicarbonate. The maintenance of precise ion gradients across cell membranes maintains osmotic pressure and pH.[21] Ions are also critical for nerve and muscle function, as action potentials in these tissues are produced by the exchange of electrolytes between the extracellular fluid and the cell's fluid, thecytosol.[22] Electrolytes enter and leave cells through proteins in the cell membrane called ion channels. For example,muscle contraction depends upon the movement of calcium, sodium and potassium through ion channels in the cell membrane and T-tubules.[23]

Transition metals are usually present as trace elements in organisms, with zinc and iron being most abundant of those.[24][25]These metals are used in some proteins as cofactors and are essential for the activity of enzymes such as catalase and oxygen-carrier proteins such as hemoglobin.[26] Metal cofactors are bound tightly to specific sites in proteins; although enzyme cofactors can be modified during catalysis, they always return to their original state by the end of the reaction catalyzed. Metal micronutrients are taken up into organisms by specific transporters and bind to storage proteins such asferritin or metallothionein when not in use.[27][28]

Catabolism[edit]

Catabolism is the set of metabolic processes that break down large molecules. These include breaking down and oxidizing food molecules. The purpose of the catabolic reactions is to provide the

energy and components needed by anabolic reactions. The exact nature of these catabolic reactions differ from organism to organism and organisms can be classified based on their sources of energy and carbon (their primary nutritional groups), as shown in the table below. Organic molecules are used as a source of energy by organotrophs, while lithotrophs use inorganic substrates and phototrophscapture sunlight as chemical energy. However, all these different forms of metabolism depend on redox reactions that involve the transfer of electrons from reduced donor molecules such as organic molecules, water, ammonia, hydrogen sulfide or ferrous ions to acceptor molecules such as oxygen, nitrate or sulfate.[29] In animals these reactions involve complex organic molecules that are broken down to simpler molecules, such as carbon dioxide and water. In photosyntheticorganisms such as plants and cyanobacteria, these electron-transfer reactions do not release energy, but are used as a way of storing energy absorbed from sunlight.[30]

Classification of organisms based on their metabolism

Energy source

sunlightphoto-

-troph

Preformed 

molecules

chemo-

Electron 

donor

organic compou

nd

organo-

inorganic compou

ndlitho-

Carbon 

source

organic compou

nd

hetero-

inorganic compou

ndauto-

The most common set of catabolic reactions in animals can be separated into three main stages. In the first, large organic molecules such as proteins, polysaccharides or lipids are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to yet smaller molecules, usually acetyl coenzyme A (acetyl-CoA), which releases some energy. Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the citric acid cycle and electron transport chain, releasing the energy that is stored by reducing the coenzyme nicotinamide adenine dinucleotide (NAD+) into NADH.

Digestion[edit]Further information: Digestion and gastrointestinal tract

Macromolecules such as starch, cellulose or proteins cannot be rapidly taken up by cells and must be broken into their smaller units before they can be used in cell metabolism. Several common classes of enzymes digest these polymers. These digestive enzymes include proteases that digest proteins into amino acids, as well as glycoside hydrolases that digest polysaccharides into simple sugars known as monosaccharides.

Microbes simply secrete digestive enzymes into their surroundings,[31][32] while animals only secrete these enzymes from specialized cells in their guts.[33] The amino acids or sugars released by these extracellular enzymes are then pumped into cells by active transport proteins.[34][35]

A simplified outline of the catabolism of proteins,carbohydrates and fats

Energy from organic compounds[edit]Further information: Cellular respiration, fermentation, carbohydrate catabolism, fat catabolism and protein catabolism

Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Carbohydrates are usually taken into cells once they have been digested into monosaccharides.[36] Once inside, the major route of breakdown is glycolysis, where sugars such as glucose andfructose are converted into pyruvate and some ATP is generated.[37]Pyruvate is an intermediate in several metabolic pathways, but the majority is converted to acetyl-CoA and fed into the citric acid cycle. Although some more ATP is generated in the citric acid cycle, the most important product is NADH, which is made from NAD+ as the acetyl-CoA is oxidized. This oxidation releases carbon dioxide as a waste product. In anaerobic conditions, glycolysis produces lactate, through the enzyme lactate dehydrogenase re-oxidizing NADH to NAD+ for re-use in glycolysis. An alternative route for glucose

breakdown is the pentose phosphate pathway, which reduces the coenzymeNADPH and produces pentose sugars such as ribose, the sugar component of nucleic acids.

Fats are catabolised by hydrolysis to free fatty acids and glycerol. The glycerol enters glycolysis and the fatty acids are broken down by beta oxidation to release acetyl-CoA, which then is fed into the citric acid cycle. Fatty acids release more energy upon oxidation than carbohydrates because carbohydrates contain more oxygen in their structures. Steroids are also broken down by some bacteria in a process similar to beta oxidation, and this breakdown process involves the release of significant amounts of acetyl-CoA, propionyl-CoA, and pyruvate, which can all be used by the cell for energy. M. tuberculosis can also grow on the lipid cholesterol as a sole source of carbon, and genes involved in the cholesterol use pathway(s) have been validated as important during various stages of the infection lifecycle of M. tuberculosis.[38]

Amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and carbon dioxide as a source of energy.[39] The oxidation pathway starts with the removal of the amino group by a transaminase. The amino group is fed into the urea cycle, leaving a deaminated carbon skeleton in the form of a keto acid. Several of these keto acids are intermediates in the citric acid cycle, for example the deamination of glutamate forms α-ketoglutarate.[40] The glucogenic amino acids can also be converted into glucose, through gluconeogenesis (discussed below).[41]

Energy transformations[edit]

Oxidative phosphorylation[edit]Further information: Oxidative phosphorylation, chemiosmosis and mitochondrion

In oxidative phosphorylation, the electrons removed from organic molecules in areas such as the protagon acid cycle are transferred to oxygen and the energy released is used to make ATP. This is done in eukaryotes by a series of proteins in the membranes of mitochondria called the electron transport chain. In prokaryotes, these proteins are found in the cell'sinner membrane.[42] These proteins use the energy released from passing electrons from reduced molecules like NADH ontooxygen to pump protons across a membrane.[43]

Mechanism of ATP synthase. ATP is shown in red, ADP and phosphate in pink and the rotating stalk subunit in

black.

Pumping protons out of the mitochondria creates a proton concentration differenceacross the membrane and generates an electrochemical gradient.[44] This force drives protons back into the mitochondrion through the base of an enzyme calledATP synthase. The flow of protons makes the stalk subunit rotate, causing the active site of the synthase domain to change shape and phosphorylate adenosine diphosphate – turning it into ATP.[17]

Energy from inorganic compounds[edit]

Further information: Microbial metabolism and nitrogen cycle

Chemolithotrophy is a type of metabolism found in prokaryotes where energy is obtained from the oxidation of inorganic compounds. These organisms can usehydrogen,[45] reduced sulfur compounds (such as sulfide, hydrogen sulfide andthiosulfate),[1] ferrous iron (FeII) [46]  or ammonia [47]  as sources of reducing power and they gain energy from the oxidation of these compounds with electron acceptors such as oxygen or nitrite.[48] These microbial processes are important in global biogeochemical cycles such asacetogenesis, nitrification and denitrification and are critical for soil fertility.[49][50]

Energy from light[edit]Further information: Phototroph, photophosphorylation, chloroplast

The energy in sunlight is captured by plants, cyanobacteria, purple bacteria, green sulfur bacteria and some protists. This process is often coupled to the conversion of carbon dioxide into organic compounds, as part of photosynthesis, which is discussed below. The energy capture and carbon fixation systems can however operate separately in prokaryotes, as purple bacteria and green sulfur bacteria can use sunlight as a source of energy, while switching between carbon fixation and the fermentation of organic compounds.[51][52]

In many organisms the capture of solar energy is similar in principle to oxidative phosphorylation, as it involves the storage of energy as a proton concentration gradient. This proton motive force then drives ATP synthesis.[17] The electrons needed to drive this electron transport chain come from light-gathering proteins called photosynthetic reaction centres orrhodopsins. Reaction centers are classed into two types depending on the type of photosynthetic pigment present, with most photosynthetic bacteria only having one type, while plants and cyanobacteria have two. [53]

In plants, algae, and cyanobacteria, photosystem II uses light energy to remove electrons from water, releasing oxygen as a waste product. The electrons then flow to the cytochrome b6f complex, which uses their energy to pump protons across thethylakoid membrane in the chloroplast.[30] These protons move back through the membrane as they drive the ATP synthase, as before. The electrons then flow through photosystem I and can then either be used to reduce the coenzyme NADP+, for use in the Calvin cycle, which is discussed below, or recycled for further ATP generation.[54]

Anabolism[edit]Further information: Anabolism

Anabolism is the set of constructive metabolic processes where the energy released by catabolism is used to synthesize complex molecules. In general, the complex molecules that make up cellular structures are constructed step-by-step from small and simple precursors. Anabolism involves three basic stages. First, the production of precursors such as amino acids, monosaccharides, isoprenoids and nucleotides, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as proteins, polysaccharides, lipids and nucleic acids.

Organisms differ in how many of the molecules in their cells they can construct for themselves. Autotrophs such as plants can construct the complex organic molecules in cells such as polysaccharides and proteins from simple molecules likecarbon dioxide and water. Heterotrophs, on the other hand, require a source of more complex substances, such as monosaccharides and amino acids, to produce these complex molecules. Organisms can be further classified by ultimate source of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation reactions.

Carbon fixation[edit]Further information: Photosynthesis, carbon fixation and chemosynthesis

Plant cells (bounded by purple walls) filled with chloroplasts (green), which are the site of photosynthesis

Photosynthesis is the synthesis of carbohydrates from sunlight and carbon dioxide(CO2). In plants, cyanobacteria and algae, oxygenic photosynthesis splits water, with oxygen produced as a waste product. This process uses the ATP and NADPH produced by the photosynthetic reaction centres, as described above, to convert CO2 into glycerate 3-phosphate, which can then be converted into glucose. This carbon-fixation reaction is carried out by the enzyme RuBisCO as part of theCalvin   – Benson cycle.[55] Three types of photosynthesis occur in plants, C3 carbon fixation, C4 carbon fixation and CAM photosynthesis. These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO2 directly, while C4 and CAM photosynthesis incorporate the CO2 into other compounds first, as adaptations to deal with intense sunlight and dry conditions. [56]

In photosynthetic prokaryotes the mechanisms of carbon fixation are more diverse. Here, carbon dioxide can be fixed by the Calvin – Benson cycle, a reversed citric acid cycle,[57] or the carboxylation of acetyl-CoA.[58][59] Prokaryotic chemoautotrophs also fix CO2 through the Calvin – Benson cycle, but use energy from inorganic compounds to drive the reaction.[60]

Carbohydrates and glycans[edit]Further information: Gluconeogenesis, glyoxylate cycle, glycogenesis and glycosylation

In carbohydrate anabolism, simple organic acids can be converted into monosaccharides such as glucose and then used to assemble polysaccharides such as starch. The generation of glucose from compounds like pyruvate, lactate, glycerol,glycerate 3-phosphate and amino acids is called gluconeogenesis. Gluconeogenesis converts pyruvate to glucose-6-phosphate through a series of intermediates, many of which are shared with glycolysis.[37] However, this pathway is not simply glycolysis run in reverse, as several steps are catalyzed by non-glycolytic enzymes. This is important as it allows the formation and breakdown of glucose to be regulated separately, and prevents both pathways from running simultaneously in a futile cycle.[61][62]

Although fat is a common way of storing energy, in vertebrates such as humans the fatty acids in these stores cannot be converted to glucose through gluconeogenesis as these organisms cannot convert acetyl-CoA into pyruvate; plants do, but animals do not, have the necessary enzymatic machinery.[63] As a result, after long-term starvation, vertebrates need to produce ketone bodies from fatty acids to replace glucose in tissues such as the brain that cannot metabolize fatty acids. [64]In other organisms such as plants and bacteria, this metabolic problem is solved using the glyoxylate cycle, which bypasses the decarboxylation step in the citric acid cycle and allows the transformation of acetyl-CoA to oxaloacetate, where it can be used for the production of glucose.[63][65]

Polysaccharides and glycans are made by the sequential addition of monosaccharides by glycosyltransferase from a reactive sugar-phosphate donor such as uridine diphosphate glucose (UDP-glucose) to an acceptor hydroxyl group on the growing polysaccharide. As any of the hydroxyl groups on the ring of the substrate can be acceptors, the polysaccharides produced can have straight or branched structures.[66] The polysaccharides produced can have structural or

metabolic functions themselves, or be transferred to lipids and proteins by enzymes called oligosaccharyltransferases.[67][68]

Fatty acids, isoprenoids and steroids[edit]Further information: Fatty acid synthesis, steroid metabolism

Simplified version of the steroid synthesis pathway with the intermediates isopentenyl

pyrophosphate (IPP), dimethylallyl pyrophosphate (DMAPP), geranyl pyrophosphate (GPP)

andsqualene shown. Some intermediates are omitted for clarity.

Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl-CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the acyl group, reduce it to an alcohol, dehydrate it to an alkene group and then reduce it again to an alkane group. The enzymes of fatty acid biosynthesis are divided into two groups: in animals and fungi, all these fatty acid synthase reactions are carried out by a single multifunctional type I protein,[69] while in plantplastids and bacteria separate type II enzymes perform each step in the pathway. [70][71]

Terpenes and isoprenoids are a large class of lipids that include the carotenoids and form the largest class of plantnatural products.[72] These compounds are made by the assembly and modification of isoprene units donated from the reactive precursors isopentenyl pyrophosphate anddimethylallyl pyrophosphate.[73] These precursors can be made in different ways. In animals and archaea, the mevalonate pathway produces these compounds from acetyl-CoA,[74] while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates.[73][75]One important reaction that uses these activated isoprene donors is steroid biosynthesis. Here, the isoprene units are joined together to make squalene and then folded up and formed into a set of rings to make lanosterol.[76] Lanosterol can then be converted into other steroids such as cholesteroland ergosterol.[76][77]

Proteins[edit]Further information: Protein biosynthesis, amino acid synthesis

Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants can synthesize all twenty, but mammals can only synthesize eleven nonessential amino acids, so nine essential amino acids must be obtained from food.[7] Some simple parasites, such as the bacteria Mycoplasma pneumoniae, lack all amino acid synthesis and take their amino acids directly from their hosts.[78] All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and glutamine. Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then transaminated to form an amino acid.[79]

Amino acids are made into proteins by being joined together in a chain of peptide bonds. Each different protein has a unique sequence of amino acid residues: this is its primary structure. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a transfer RNA molecule through an esterbond. This aminoacyl-tRNA precursor is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase.[80] This aminoacyl-tRNA is then a substrate for the ribosome, which joins the amino acid onto the elongating protein chain, using the sequence information in a messenger RNA.[81]

Nucleotide synthesis and salvage[edit]Further information: Nucleotide salvage, pyrimidine biosynthesis, and purine metabolism

Nucleotides are made from amino acids, carbon dioxide and formic acid in pathways that require large amounts of metabolic energy.[82] Consequently, most organisms have efficient systems to salvage preformed nucleotides.[82][83] Purines are synthesized as nucleosides (bases attached to ribose).[84] Both adenine and guanine are made from the precursor nucleoside inosine monophosphate, which is synthesized using atoms from the amino acids glycine, glutamine, and aspartic acid, as well as formate transferred from the coenzyme tetrahydrofolate. Pyrimidines, on the other hand, are synthesized from the base orotate, which is formed from glutamine and aspartate.[85]

Xenobiotics and redox metabolism[edit]Further information: Xenobiotic metabolism, drug metabolism, Alcohol metabolism and antioxidants

All organisms are constantly exposed to compounds that they cannot use as foods and would be harmful if they accumulated in cells, as they have no metabolic function. These potentially damaging compounds are called xenobiotics.[86]Xenobiotics such as synthetic drugs, natural poisons and antibiotics are detoxified by a set of xenobiotic-metabolizing enzymes. In humans, these include cytochrome P450 oxidases,[87] UDP-glucuronosyltransferases,[88] and glutathione   S - transferases.[89] This system of enzymes acts in three stages to firstly oxidize the xenobiotic (phase I) and then conjugate water-soluble groups onto the molecule (phase II). The modified water-soluble xenobiotic can then be pumped out of cells and in multicellular organisms may be further metabolized before being excreted (phase III). In ecology, these reactions are particularly important in microbial biodegradation of pollutants and the bioremediation of contaminated land and oil spills.[90]Many of these microbial reactions are shared with multicellular organisms, but due to the incredible diversity of types of microbes these organisms are able to deal with a far wider range of xenobiotics than multicellular organisms, and can degrade even persistent organic pollutants such as organochloride compounds.[91]

A related problem for aerobic organisms is oxidative stress.[92] Here, processes including oxidative phosphorylation and the formation of disulfide bonds during protein folding produce reactive oxygen species such as hydrogen peroxide.[93] These damaging oxidants are removed by antioxidant metabolites such as glutathione and enzymes such as catalases andperoxidases.[94][95]

Thermodynamics of living organisms[edit]Further information: Biological thermodynamics

Living organisms must obey the laws of thermodynamics, which describe the transfer of heat and work. The second law of thermodynamics states that in any closed system, the amount of entropy (disorder) cannot decrease. Although living organisms' amazing complexity appears to contradict this law, life is possible as all organisms are open systems that exchange matter and energy with their surroundings. Thus living systems are not in equilibrium, but instead are dissipative systems that maintain their state of high complexity by causing a larger increase in the entropy of their environments.[96] The metabolism of a cell achieves this by coupling the spontaneous processes of catabolism to the non-spontaneous processes of anabolism. In thermodynamic terms, metabolism maintains order by creating disorder.[97]

Regulation and control[edit]Further information: Metabolic pathway, metabolic control analysis, hormone, regulatory enzymes, and cell signaling

As the environments of most organisms are constantly changing, the reactions of metabolism must be finely regulated to maintain a constant set of conditions within cells, a condition called homeostasis.[98][99] Metabolic regulation also allows organisms to respond to signals and interact actively with their environments.[100] Two closely linked concepts are important for understanding how metabolic pathways are controlled. Firstly, the regulation of an enzyme in a pathway is how its activity is increased and decreased in response to signals. Secondly, the control exerted by this enzyme is the effect that these changes in its activity have on the overall rate of the pathway (the flux through the pathway).[101] For example, an enzyme may show large changes in activity (i.e. it is highly regulated) but if these changes have little effect on the flux of a metabolic pathway, then this enzyme is not involved in the control of the pathway. [102]

Effect of insulin on glucose uptake and metabolism. Insulin binds to its receptor (1), which in turn starts

many protein activation cascades (2). These include: translocation of Glut-4 transporter to the plasma

membrane and influx of glucose (3),glycogen synthesis (4), glycolysis (5) and fatty acidsynthesis (6).

There are multiple levels of metabolic regulation. In intrinsic regulation, the metabolic pathway self-regulates to respond to changes in the levels of substrates or products; for example, a decrease in

the amount of product can increase the flux through the pathway to compensate.[101] This type of regulation often involves allosteric regulation of the activities of multiple enzymes in the pathway.[103]Extrinsic control involves a cell in a multicellular organism changing its metabolism in response to signals from other cells. These signals are usually in the form of soluble messengers such as hormones andgrowth factors and are detected by specific receptors on the cell surface.[104] These signals are then transmitted inside the cell bysecond messenger systems that often involved the phosphorylation of proteins.[105]

A very well understood example of extrinsic control is the regulation of glucose metabolism by the hormone insulin.[106] Insulin is produced in response to rises in blood glucose levels. Binding of the hormone to insulin receptors on cells then activates a cascade ofprotein kinases that cause the cells to take up glucose and convert it into storage molecules such as fatty acids andglycogen.[107] The metabolism of glycogen is controlled by activity of phosphorylase, the enzyme that breaks down glycogen, and glycogen synthase, the enzyme that makes it. These enzymes are regulated in a reciprocal fashion, with phosphorylation inhibiting glycogen synthase, but activating phosphorylase. Insulin causes glycogen synthesis by activatingprotein phosphatases and producing a decrease in the phosphorylation of these enzymes.[108]

Evolution[edit]Further information: Molecular evolution and phylogenetics

Evolutionary tree showing the common ancestry of organisms from all three domains of life. Bacteria are

colored blue, eukaryotes red, andarchaea green. Relative positions of some of the phyla included are shown

around the tree.

The central pathways of metabolism described above, such as glycolysis and the citric acid cycle, are present in all three domains of living things and were present in the last universal ancestor.[3]

[109] This universal ancestral cell was prokaryotic and probably amethanogen that had extensive amino acid, nucleotide, carbohydrate and lipid metabolism.[110][111] The retention of these ancient pathways during laterevolution may be the result of these reactions having been an optimal solution to their particular metabolic problems, with pathways such as glycolysis and the citric acid cycle producing their end products highly efficiently and in a minimal number of steps.[4][5]Mutation changes that affect non-coding DNA segments may merely affect the metabolic efficiency of the individual for

whom the mutation occurs.[112] The first pathways of enzyme-based metabolism may have been parts of purine nucleotide metabolism, while previous metabolic pathways were a part of the ancient RNA world.[113]

Many models have been proposed to describe the mechanisms by which novel metabolic pathways evolve. These include the sequential addition of novel enzymes to a short ancestral pathway, the duplication and then divergence of entire pathways as well as the recruitment of pre-existing enzymes and their assembly into a novel reaction pathway.[114] The relative importance of these mechanisms is unclear, but genomic studies have shown that enzymes in a pathway are likely to have a shared ancestry, suggesting that many pathways have evolved in a step-by-step fashion with novel functions created from pre-existing steps in the pathway.[115] An alternative model comes from studies that trace the evolution of proteins' structures in metabolic networks, this has suggested that enzymes are pervasively recruited, borrowing enzymes to perform similar functions in different metabolic pathways (evident in the MANET database)[116] These recruitment processes result in an evolutionary enzymatic mosaic.[117] A third possibility is that some parts of metabolism might exist as "modules" that can be reused in different pathways and perform similar functions on different molecules.[118]

As well as the evolution of new metabolic pathways, evolution can also cause the loss of metabolic functions. For example, in some parasites metabolic processes that are not essential for survival are lost and preformed amino acids, nucleotides and carbohydrates may instead be scavenged from the host.[119] Similar reduced metabolic capabilities are seen inendosymbiotic organisms.[120]

Investigation and manipulation[edit]Further information: Protein methods, proteomics, metabolomics and metabolic network modelling

Metabolic network of the Arabidopsis thaliana citric acid cycle. Enzymes and metabolites are shown as red

squares and the interactions between them as black lines.

Classically, metabolism is studied by a reductionist approach that focuses on a single metabolic pathway. Particularly valuable is the use of radioactive tracers at the whole-organism, tissue and cellular levels, which define the paths from precursors to final products by identifying radioactively

labelled intermediates and products.[121] The enzymes that catalyze these chemical reactions can then be purified and their kineticsand responses to inhibitors investigated. A parallel approach is to identify the small molecules in a cell or tissue; the complete set of these molecules is called the metabolome. Overall, these studies give a good view of the structure and function of simple metabolic pathways, but are inadequate when applied to more complex systems such as the metabolism of a complete cell.[122]

An idea of the complexity of the metabolic networks in cells that contain thousands of different enzymes is given by the figure showing the interactions between just 43 proteins and 40 metabolites to the right: the sequences of genomes provide lists containing anything up to 45,000 genes.[123] However, it is now possible to use this genomic data to reconstruct complete networks of biochemical reactions and produce more holistic mathematical models that may explain and predict their behavior.[124] These models are especially powerful when used to integrate the pathway and metabolite data obtained through classical methods with data on gene expression from proteomicand DNA microarray studies.[125] Using these techniques, a model of human metabolism has now been produced, which will guide future drug discovery and biochemical research.[126] These models are now used in network analysis, to classify human diseases into groups that share common proteins or metabolites.[127][128]

Bacterial metabolic networks are a striking example of bow-tie [129] [130] [131]  organization, an architecture able to input a wide range of nutrients and produce a large variety of products and complex macromolecules using a relatively few intermediate common currencies.

A major technological application of this information is metabolic engineering. Here, organisms such as yeast, plants orbacteria are genetically modified to make them more useful in biotechnology and aid the production of drugs such asantibiotics or industrial chemicals such as 1,3-propanediol and shikimic acid.[132] These genetic modifications usually aim to reduce the amount of energy used to produce the product, increase yields and reduce the production of wastes. [133]

History[edit]Further information: History of biochemistry and history of molecular biology

Santorio Santorio in his steelyard balance, fromArs de statica medicina, first published 1614

The term metabolism is derived from the Greek Μεταβολισμός – "Metabolismos" for "change", or "overthrow".[134] The first documented references of metabolism were made by Ibn al-Nafis in his 1260 AD work titled Al-Risalah al-Kamiliyyah fil Siera al-Nabawiyyah (The Treatise of Kamil on the Prophet's Biography) which included the following phrase "Both the body and its parts are in a

continuous state of dissolution and nourishment, so they are inevitably undergoing permanent change."[135] The history of the scientific study of metabolism spans several centuries and has moved from examining whole animals in early studies, to examining individual metabolic reactions in modern biochemistry. The first controlled experiments in human metabolism were published by Santorio Santorio in 1614 in his book Ars de statica medicina.[136] He described how he weighed himself before and after eating, sleep, working, sex, fasting, drinking, and excreting. He found that most of the food he took in was lost through what he called "insensible perspiration".

In these early studies, the mechanisms of these metabolic processes had not been identified and a vital force was thought to animate living tissue.[137] In the 19th century, when studying thefermentation of sugar to alcohol by yeast, Louis Pasteur concluded that fermentation was catalyzed by substances within the yeast cells he called "ferments". He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells."[138] This discovery, along with the publication by Friedrich Wöhler in 1828 of a paper on the chemical synthesis ofurea,[139] and is notable for being the first organic compound prepared from wholly inorganic precursors. This proved that the organic compounds and chemical reactions found in cells were no different in principle than any other part of chemistry.

It was the discovery of enzymes at the beginning of the 20th century by Eduard Buchner that separated the study of the chemical reactions of metabolism from the biological study of cells, and marked the beginnings of biochemistry.[140] The mass of biochemical knowledge grew rapidly throughout the early 20th century. One of the most prolific of these modern biochemists was Hans Krebs who made huge contributions to the study of metabolism.[141] He discovered the urea cycle and later, working with Hans Kornberg, the citric acid cycle and the glyoxylate cycle.[142][65] Modern biochemical research has been greatly aided by the development of new techniques such as chromatography, X-ray diffraction, NMR spectroscopy,radioisotopic labelling, electron microscopy and molecular dynamics simulations. These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells.

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Molecular biology /məˈlɛkjʊlər/ concerns the molecular basis of biologicalactivity between the various systems of a cell, including the interactions between DNA, RNA and proteins and their biosynthesis, as well as the regulation of these interactions. Writing in Nature in 1961, William Astburydescribed molecular biology as:

"...not so much a technique as an approach, an approach from the viewpoint of the so-called basic sciences with the leading idea of searching below the large-scale manifestations of classical biology for the corresponding molecular plan. It is concerned particularly with the forms of biological molecules and [...] is predominantly three-dimensional and structural—which does not mean, however, that it is merely a refinement of morphology. It must at the same time inquire into genesis and function."[1]

Contents  [hide] 

1 Relationship to other biological sciences 2 Techniques of molecular biology

o 2.1 Molecular cloning o 2.2 Polymerase chain reaction (PCR) o 2.3 Gel electrophoresis o 2.4 Macromolecule blotting and probing

2.4.1 Southern blotting 2.4.2 Northern blotting 2.4.3 Western blotting 2.4.4 Eastern blotting

o 2.5 Microarrays o 2.6 Allele-specific oligonucleotide o 2.7 Antiquated technologies

3 History 4 Clinical significance 5 See also 6 References 7 Further reading 8 External links

Relationship to other biological sciences[edit]

Schematic relationship betweenbiochemistry, genetics and molecular biology

Researchers in molecular biology use specific techniques native to molecular biology but increasingly combine these with techniques and ideas from genetics andbiochemistry. There is not a defined line between these disciplines. The figure to the right 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 live 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 ofbiochemistry.

Genetics  is the study of the effect of genetic differences on organisms. This can often be inferred by the absence of a normal component (e.g. one gene). The study of "mutants" – organisms which lack one or more functional components with respect to the so-called "wild type" or normal phenotype. Genetic interactions (epistasis) can often confound simple interpretations of such "knockout" studies.

Molecular biology is the study of molecular underpinnings of the processes of replication, transcription, translation, and cell function. 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.

Much of the work in molecular biology is quantitative, and recently much work has been done at the interface of molecular biology and computer science in bioinformatics and computational biology. As of the early 2000s, the study of gene structure and function, molecular genetics, has been among the most prominent sub-field of molecular biology.

Increasingly many other loops of biology focus on molecules, either directly studying their interactions in their own right such as in cell biology and developmental biology, or indirectly, where the techniques of molecular biology are used to infer historical attributes of populations or species, as in fields in evolutionary biology such as population genetics andphylogenetics. There is also a long tradition of studying biomolecules "from the ground up" in biophysics.

Techniques of molecular biology[edit]

Since the late 1950s and early 1960s, molecular biologists have learned to characterize, isolate, and manipulate the molecular components of cells and organisms. These components include DNA, the repository of genetic information; RNA, a close relative of DNA whose functions range from serving

as a temporary working copy of DNA to actual structural and enzymatic functions as well as a functional and structural part of the translational apparatus, the ribosome; and proteins, the major structural and enzymatic type of molecule in cells.

For more extensive list on protein methods, see protein methods. For more extensive list on nucleic acid methods, seenucleic acid methods.

Molecular cloning[edit]Main article: Molecular cloning

One of the most basic techniques of molecular biology to study protein function is molecular cloning. In this technique, DNA coding for a protein of interest is cloned (using PCR and/or restriction enzymes) into a plasmid (known as an expression vector). A vector has 3 distinctive features: an origin of replication, a multiple cloning site (MCS), and a selective marker (usually antibiotic resistance). The origin of replication will have promoter regions upstream from the replication/transcriptionstart site.

This plasmid can be inserted into either bacterial or animal cells. Introducing DNA into bacterial cells can be done bytransformation (via uptake of naked DNA), conjugation (via cell-cell contact) or by transduction (via viral vector). Introducing DNA into eukaryotic cells, such as animal cells, by physical or chemical means is called transfection. Several different transfection techniques are available, such as calcium phosphate transfection, electroporation, microinjection and liposome transfection. DNA can also be introduced into eukaryotic cells using viruses or bacteria as carriers, the latter is sometimes called bactofection and in particular uses Agrobacterium tumefaciens. The plasmid may be integrated into the genome, resulting in a stable transfection, or may remain independent of the genome, called transient transfection.

In either case, DNA coding for a protein of interest is now inside a cell, and the protein can now be expressed. A variety of systems, such as inducible promoters and specific cell-signaling factors, are available to help express the protein of interest at high levels. Large quantities of a protein can then be extracted from the bacterial or eukaryotic cell. The protein can be tested for enzymatic activity under a variety of situations, the protein may be crystallized so its tertiary structure can be studied, or, in the pharmaceutical industry, the activity of new drugs against the protein can be studied.

Polymerase chain reaction (PCR)[edit]Main article: Polymerase chain reaction

Polymerase chain reaction is an extremely versatile technique for copying DNA. In brief, PCR allows a specific DNA sequence to be copied or modified in predetermined ways. The reaction is extremely powerful and under perfect conditions could amplify 1 DNA molecule to become 1.07 Billion molecules in less than 2 hours. The PCR technique can be used to introduce restriction enzyme sites to ends of DNA molecules, or to mutate (change) particular bases of DNA, the latter is a method referred to as site-directed mutagenesis. PCR can also be used to determine whether a particular DNA fragment is found in a cDNA library. PCR has many variations, like reverse transcription PCR (RT-PCR) for amplification of RNA, and, more recently, quantitative PCR which allow for quantitative measurement of DNA or RNA molecules.

Gel electrophoresis[edit]Main article: Gel electrophoresis

Gel electrophoresis is one of the principal tools of molecular biology. The basic principle is that DNA, RNA, and proteins can all be separated by means of an electric field and size. In agarose gel electrophoresis, DNA and RNA can be separated on the basis of size by running the DNA through an electrically charged agarose gel. Proteins can be separated on the basis of size by using

an SDS-PAGE gel, or on the basis of size and their electric charge by using what is known as a 2D gel electrophoresis.

Macromolecule blotting and probing[edit]The terms northern, western and eastern blotting are derived from what initially was a molecular biology joke that played on the term Southern blotting, after the technique described by Edwin Southern for the hybridisation of blotted DNA. Patricia Thomas, developer of the RNA blot which then became known as the northern blot, actually didn't use the term.[2] Further combinations of these techniques produced such terms as southwesterns (protein-DNA hybridizations), northwesterns (to detect protein-RNA interactions) and farwesterns (protein-protein interactions), all of which are presently found in the literature.

Southern blotting[edit]Main article: Southern blot

Named after its inventor, biologist Edwin Southern, the Southern blot is a method for probing for the presence of a specific DNA sequence within a DNA sample. DNA samples before or after restriction enzyme (restriction endonuclease) digestion are separated by gel electrophoresis and then transferred to a membrane by blotting via capillary action. The membrane is then exposed to a labeled DNA probe that has a complement base sequence to the sequence on the DNA of interest. Most original protocols used radioactive labels, however non-radioactive alternatives are now available. Southern blotting is less commonly used in laboratory science due to the capacity of other techniques, such as PCR, to detect specific DNA sequences from DNA samples. These blots are still used for some applications, however, such as measuring transgenecopy number in transgenic mice, or in the engineering of gene knockout embryonic stem cell lines.

Northern blotting[edit]Main article: Northern blot

The northern blot is used to study the expression patterns of a specific type of RNA molecule as relative comparison among a set of different samples of RNA. It is essentially a combination of denaturing RNA gel electrophoresis, and a blot. In this process RNA is separated based on size and is then transferred to a membrane that is then probed with a labeledcomplement of a sequence of interest. The results may be visualized through a variety of ways depending on the label used; however, most result in the revelation of bands representing the sizes of the RNA detected in sample. The intensity of these bands is related to the amount of the target RNA in the samples analyzed. The procedure is commonly used to study when and how much gene expression is occurring by measuring how much of that RNA is present in different samples. It is one of the most basic tools for determining at what time, and under what conditions, certain genes are expressed in living tissues.

Western blotting[edit]Main article: Western blot

Antibodies to most proteins can be created by injecting small amounts of the protein into an animal such as a mouse, rabbit, sheep, or donkey (polyclonal antibodies) or produced in cell culture (monoclonal antibodies). These antibodies can be used for a variety of analytical and preparative techniques.

In western blotting, proteins are first separated by size, in a thin gel sandwiched between two glass plates in a technique known as SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis). The proteins in the gel are then transferred to a polyvinylidene fluoride (PVDF), nitrocellulose, nylon, or other support membrane. This membrane can then be probed with solutions of antibodies. Antibodies that specifically bind to the protein of interest can then be visualized by a variety of techniques, including colored products, chemiluminescence, or autoradiography. Often,

the antibodies are labeled with enzymes. When a chemiluminescent substrate is exposed to the enzyme it allows detection. Using western blotting techniques allows not only detection but also quantitative analysis.

Analogous methods to western blotting can be used to directly stain specific proteins in live cells or tissue sections. However, these immunostaining methods, such as FISH, are used more often in cell biology research.

Eastern blotting[edit]Main article: Eastern blot

The Eastern blotting technique is used to detect post-translational modification of proteins.[3] Proteins blotted on to the PVDF or nitrocellulose membrane are probed for modifications using specific substrates.

Microarrays[edit]Main article: DNA microarray

A DNA microarray is a collection of spots attached to a solid support such as a microscope slide where each spot contains one or more single-stranded DNA oligonucleotide fragment. Arrays make it possible to put down large quantities of very small (100 micrometre diameter) spots on a single slide. Each spot has a DNA fragment molecule that is complementary to a single DNA sequence (similar to Southern blotting). A variation of this technique allows the gene expression of an organism at a particular stage in development to be qualified (expression profiling). In this technique the RNA in a tissue is isolated and converted to labeled cDNA. This cDNA is then hybridized to the fragments on the array and visualization of the hybridization can be done. Since multiple arrays can be made with exactly the same position of fragments they are particularly useful for comparing the gene expression of two different tissues, such as a healthy and cancerous tissue. Also, one can measure what genes are expressed and how that expression changes with time or with other factors. For instance, the common baker's yeast, Saccharomyces cerevisiae, contains about 7000 genes; with a microarray, one can measure qualitatively how each gene is expressed, and how that expression changes, for example, with a change in temperature. There are many different ways to fabricate microarrays; the most common are silicon chips, microscope slides with spots of ~ 100 micrometre diameter, custom arrays, and arrays with larger spots on porous membranes (macroarrays). There can be anywhere from 100 spots to more than 10,000 on a given array.

Arrays can also be made with molecules other than DNA. For example, an antibody array can be used to determine whatproteins or bacteria are present in a blood sample.

Allele-specific oligonucleotide[edit]Allele-specific oligonucleotide (ASO) is a technique that allows detection of single base mutations without the need for PCR or gel electrophoresis. Short (20-25 nucleotides in length), labeled probes are exposed to the non-fragmented target DNA. Hybridization occurs with high specificity due to the short length of the probes and even a single base change will hinder hybridization. The target DNA is then washed and the labeled probes that didn't hybridize are removed. The target DNA is then analyzed for the presence of the probe via radioactivity or fluorescence. In this experiment, as in most molecular biology techniques, a control must be used to ensure successful experimentation. The Illumina Methylation Assay is an example of a method that takes advantage of the ASO technique to measure one base pair differences in sequence.[citation needed]

Antiquated technologies[edit]In molecular biology, procedures and technologies are continually being developed and older technologies abandoned. For example, before the advent of DNA gel

electrophoresis (agarose or polyacrylamide), the size of DNA molecules was typically determined by rate sedimentation in sucrose gradients, a slow and labor-intensive technique requiring expensive instrumentation; prior to sucrose gradients, viscometry was used.

Aside from their historical interest, it is often worth knowing about older technology, as it is occasionally useful to solve another new problem for which the newer technique is inappropriate.

History[edit]Main article: History of molecular biology

While molecular biology was established in the 1930s, the term was coined by Warren Weaver in 1938. Weaver was the director of Natural Sciences for the Rockefeller Foundation at the time and believed that biology was about to undergo a period of significant change given recent advances in fields such as X-ray crystallography. He therefore channeled significant amounts of (Rockefeller Institute) money into biological fields.

Clinical significance[edit]

Clinical research and medical therapies arising from molecular biology are partly covered under gene therapy[citation needed]. The use of molecular biology or molecular cell biology approaches in medicine is now called molecular medicine. Molecular biology also plays important role in understanding formations, actions, regulations of various parts of cells which can be used efficiently for targeting new drugs, diagnosis of disease, physiology of the Cell.

Multi-state modeling of biomoleculesFrom Wikipedia, the free encyclopedia

Multi-state modeling of biomolecules refers to a series of techniques used to represent and compute the behaviour ofbiological molecules or complexes that can adopt a large number of possible functional states.

Biological signaling systems often rely on complexes of biological macromolecules that can undergo several functionally significant modifications that are mutually compatible. Thus, they can exist in a very large number of functionally different states. Modeling such multi-state systems poses two problems: The problem of how to describe and specify a multi-state system (the "specification problem") and the problem of how to use a computer to simulate the progress of the system over time (the "computation problem"). To address the specification problem, modelers have in recent years moved away from explicit specification of all possible states, and towards rule-based formalisms that allow for implicit model specification, including the κ-calculus,[1] BioNetGen,[2][3]

[4][5] the Allosteric Network Compiler[6] and others.[7][8] To tackle the computation problem, they have turned to particle-based methods that have in many cases proved more computationally efficient than population-based methods based on ordinary differential equations, partial differential equations, or the Gillespie stochastic simulation algorithm.[9][10] Given current computing technology, particle-based methods are sometimes the only possible option. Particle-based simulators further fall into two categories: Non-spatial simulators such as StochSim,[11] DYNSTOC,[12]RuleMonkey,[9][13] and NFSim[14] and spatial simulators, including Meredys,[15] SRSim[16][17] and MCell.[18][19][20] Modelers can thus choose from a variety of tools; the best choice depending on the particular problem. Development of faster and more powerful methods is ongoing, promising the ability to simulate ever more complex signaling processes in the future.

Contents  [hide] 

1 Introduction o 1.1 Multi-state biomolecules in signal transduction o 1.2 Examples of combinatorial explosion o 1.3 Specification vs computation

2 The specification problem o 2.1 Explicit specification o 2.2 Rule-based model specification

3 The computation problem o 3.1 Population-based rule evaluation o 3.2 Particle-based rule evaluation o 3.3 Non-spatial particle-based methods o 3.4 Spatial particle-based methods

4 Examples of multi-state models in biology 5 See also 6 References

Introduction[edit]

Multi-state biomolecules in signal transduction[edit]In living cells, signals are processed by networks of proteins that can act as complex computational devices.[21] These networks rely on the ability of single proteins to exist in a variety of functionally different states achieved through multiple mechanisms, including posttranslational modifications, ligand binding, conformational change, or formation of newcomplexes.[21][22][23]

[24] Similarly, nucleic acids can undergo a variety of transformations, including protein binding, binding of other nucleic acids, conformational change and DNA methylation.

In addition, several types of modifications can co-exist, exerting a combined influence on a biological macromolecule at any given time. Thus, a biomolecule or complex of biomolecules can often adopt a very large number of functionally distinct states. The number of states scales exponentially with the number of possible modifications, a phenomenon known as "combinatorial explosion".[24] This is of concern for computational biologists who model or simulate such biomolecules, because it raises questions about how such large numbers of states can be represented and simulated.

Examples of combinatorial explosion[edit]Biological signaling networks incorporate a wide array of reversible interactions, post-translational modifications andconformational changes. Furthermore, it is common for a protein to be composed of several - identical or nonidentical -subunits, and for several proteins and/or nucleic acid species to assemble into larger complexes. A molecular species with several of those features can therefore exist in a large number of possible states.

For instance, it has been estimated that the yeast scaffold protein Ste5 can be a part of 25666 unique protein complexes.[22]In E. coli, chemotaxis receptors of four different kinds interact in groups of three, and each individual receptor can exist in at least two possible conformations and has up to eight methylation sites,[23] resulting in billions of potential states. The proteinkinase CaMKII is a dodecamer of twelve catalytic subunits,[25] arranged in two hexameric rings.[26] Each subunit can exist in at least two distinct conformations, and each subunit features various phosphorylation and ligand binding sites. A recent model[27] incorporated conformational states, two phosphorylation sites and two modes of binding calcium/calmodulin, for a total of around one billion possible states per hexameric ring. A model of coupling of the EGF receptor to a MAP kinasecascade presented by

Danos and colleagues[28] accounts for   distinct molecular species, yet the authors note several points at which the model could be further extended. A more recent model of ErbB receptor signalling even accounts for more than one googol ( ) distinct molecular species.[29] The problem of combinatorial explosion is also relevant tosynthetic biology, with a recent model of a relatively simple synthetic eukaryotic gene circuit featuring 187 species and 1165reactions.[30]

Of course, not all of the possible states of a multi-state molecule or complex will necessarily be populated. Indeed, in systems where the number of possible states is far greater than that of molecules in the compartment (e.g. the cell), they cannot be. In some cases, empirical information can be used to rule out certain states if, for instance, some combinations of features are incompatible. In the absence of such information, however, all possible states need to be considered a priori. In such cases, computational modeling can be used to uncover to what extent the different states are populated.

The existence (or potential existence) of such large numbers of molecular species is a combinatorial phenomenon: It arises from a relatively small set of features or modifications (such as post-translational modification or complex formation) that combine to dictate the state of the entire molecule or complex, in the same way that the existence of just a few choices in acoffee shop (small, medium or large, with or without milk, decaf or not, extra shot of espresso) quickly leads to a large number of possible beverages (24 in this case; each additional binary choice will double that number). Although it is difficult for us to grasp the total numbers of possible combinations, it is usually not conceptually difficult to understand the (much smaller) set of features or modifications and the effect each of them has on the function of the biomolecule. The rate at which a molecule undergoes a particular reaction will usually depend mainly on a single feature or a small subset of features. It is the presence or absence of those features that dictates the reaction rate. The reaction rate is the same for two molecules that differ only in features which do not affect this reaction. Thus, the number of parameters will be much smaller than the number of reactions. (In the coffee shop example, adding an extra shot of espresso will cost 40 cent, no matter what size the beverage is and whether or not it has milk in it). It is such "local rules" that are usually discovered in laboratory experiments. Thus, a multi-state model can be conceptualised in terms of combinations of modular features and local rules. This means that even a model that can account for a vast number of molecular species and reactions is not necessarily conceptually complex.

Specification vs computation[edit]

Figure 1: An overview of tools discussed here that are used for the rule-based specification and particle-based

evaluation (spatial or non-spatial) of multi-state biomolecules.

The combinatorial complexity of signaling systems involving multi-state proteins poses two kinds of problems. The first problem is concerned with how such a system can be specified; i.e. how a modeler can specify all complexes, all changes those complexes undergo and all parameters and conditions governing those changes in a robust and efficient way. This problem is called the "specification problem". The second problem concerns computation. It asks questions about whether

a combinatorially complex model, once specified, is computationally tractable, given the large number of states and the even larger number of possible transitions between states, whether it can be stored electronically, and whether it can be evaluated in a reasonable amount of computing time. This problem is called the "computation problem". Among the approaches that have been proposed to tackle combinatorial complexity in multi-state modeling, some are mainly concerned with addressing the specification problem, some are focused on finding effective methods of computation. Some tools address both specification and computation. The sections below discuss rule-based approaches to the specification problem and particle-based approaches to solving the computation problem. A list of the tools discussed here is presented in Figure 1. A comprehensive overview and discussion of various tools available for multi-state modeling can be found in Chylek et al.[31]

The specification problem[edit]

Explicit specification[edit]The most naïve way of specifying, e.g., a protein in a biological model is to specify each of its states explicitly and use each of them as a molecular species in a simulation framework that allows transitions from state to state. For instance, if a protein can be ligand-bound or not, exist in two conformational states (e.g. open or closed) and be located in two possible subcellular areas (e.g. cytosolic or membrane-bound), then the eight possible resulting states can be explicitly enumerated as:

bound, open, cytosol bound, open, membrane bound, closed, cytosol bound, closed, membrane unbound, open, cytosol unbound, open, membrane unbound, closed, cytosol unbound, closed, membrane

Enumerating all possible states is a lengthy and potentially error-prone process. For macromolecular complexes that can adopt multiple states, enumerating each state quickly becomes tedious, if not impossible. Moreover, the addition of a single additional modification or feature to the model of the complex under investigation will double the number of possible states (if the modification is binary), and it will more than double the number of transitions that need to be specified.

Rule-based model specification[edit]It is clear that an explicit description, which lists all possible molecular species (including all their possible states), all possible reactions or transitions these species can undergo, and all parameters governing these reactions, very quickly becomes unwieldy as the complexity of the biological system increases. Modelers have therefore looked for implicit, rather than explicit, ways of specifying a biological signaling system. An implicit description is one that groups reactions and parameters that apply to many types of molecular species into one reaction template. It might also add a set of conditions that govern reaction parameters, i.e. the likelihood or rate at which a reaction occurs, or whether it occurs at all. Only properties of the molecule or complex that matter to a given reaction (either affecting the reaction or being affected by it) are explicitly mentioned, and all other properties are ignored in the specification of the reaction.

For instance, the rate of ligand dissociation from a protein might depend on the conformational state of the protein, but not on its subcellular localization. An implicit description would therefore list two dissociation processes (with different rates, depending on conformational state), but would ignore

attributes referring to subcellular localization, because they do not affect the rate of ligand dissociation, nor are they affected by it. This specification rule has been summarized as "Don't care, don't write".[28]

Since it is not written in terms of reactions, but in terms of more general "reaction rules" encompassing sets of reactions, this kind of specification is often called "rule-based".[4] This description of the system in terms of modular rules relies on the assumption that only a subset of features or attributes are relevant for a particular reaction rule. Where this assumption holds, a set of reactions can be coarse-grained into one reaction rule. This coarse-graining preserves the important properties of the underlying reactions. For instance, if the reactions are based on chemical kinetics, so are the rules derived from them.

Many rule-based specification methods exist. In general, the specification of a model is a separate task from the execution of the simulation. Therefore, among the existing rule-based model specification systems,[4] some concentrate on model specification only, allowing the user to then export the specified model into a dedicated simulation engine. However, many solutions to the specification problem also contain a method of interpreting the specified model.[3] This is done by providing a method to simulate the model or a method to convert it into a form that can be used for simulations in other programs.

An early rule-based specification method is the κ-calculus,[1] a process algebra that can be used to encode macromolecules with internal states and binding sites and to specify rules by which they interact. A review of κ is provided by Danos et al.[28]The κ-calculus is merely concerned with providing a language to encode multi-state models, not with interpreting the models themselves. A simulator compatible with Kappa is KaSim.[32][33]

BioNetGen is a software suite that provides both specification and simulation capacities. [2][3][4][5] Rule-based models can be written down using a specified syntax, the BioNetGen language (BNGL). [4] The underlying concept is to represent biochemical systems as graphs, where molecules are represented as nodes (or collections of nodes) and chemical bonds as edges. A reaction rule, then, corresponds to a graph rewriting rule.[3] BNGL provides a syntax for specifying these graphs and the associated rules as structured strings.[4] BioNetGen can then use these rules to generate ordinary differential equations (ODEs) to describe each biochemical reaction. Alternatively, it can generate a list of all possible species and reactions in SBML,[34][35] which can then be exported to simulation software packages that can read SBML. One can also make use of BioNetGen's own ODE-based simulation software and its capability to generate reactions on-the-fly during a stochastic simulation.[5] In addition, a model specified in BNGL can be read by other simulation software, such as DYNSTOC,[12] RuleMonkey,[13] and NFSim.[14]

Another tool that generates full reaction networks from a set of rules is the Allosteric Network Compiler (ANC).[6]Conceptually, ANC sees molecules as allosteric devices with a Monod-Wyman-Changeux (MWC) type regulation mechanism,[36] whose interactions are governed by their internal state, as well as by external modifications. A very useful feature of ANC is that it automatically computes dependent parameters, thereby imposing thermodynamic correctness.[37]

An extension of the κ-calculus is provided by React(C).[38] The authors of React C show that it can express the stochastic π calculus.[39] They also provide a stochastic simulation algorithm based on the Gillespie stochastic algorithm [40] for models specified in React(C).[38]

ML-Rules[41] is similar to React(C), but provides the added possibility of nesting: A component species of the model, with all its attributes, can be part of a higher-order component species. This enables ML-Rules to capture multi-level models that can bridge the gap between, for instance, a series of biochemical processes and the macroscopic behaviour of a whole cell or group of cells. For instance, Maus et al. have provided a proof-of-concept model of cell division in fission yeast that includes cyclin/cdc2 binding and activation, pheromone secretion and diffusion, cell division and movement of cells.[41]Models specified in ML-Rules can be simulated using the James II simulation

framework.[42] A similar nested language to represent multi-level biological systems has been proposed by Oury and Plotkin.[43]

Yang et al.[8] have proposed a specification formalism based on finite automata. Models specified in their Molecular Finite Automata (MFA) framework can then be used to generate and simulate a system of ODEs or for stochastic simulation using a kinetic Monte Carlo algorithm.

Some rule-based specification systems and their associated network generation and simulation tools have been designed to accommodate spatial heterogeneity, in order to allow for the realistic simulation of interactions within biological compartments. For instance, the Simmune project[44]

[45] includes a spatial component: Users can specify their multi-state biomolecules and interactions within membranes or compartments of arbitrary shape. The reaction volume is then divided into interfacing voxels, and a separate reaction network generated for each of these subvolumes.

The Stochastic Simulator Compiler (SSC)[46] allows for rule-based, modular specification of interacting biomolecules in regions of arbitrarily complex geometries. Again, the system is represented using graphs, with chemical interactions or diffusion events formalised as graph-rewriting rules.[46] The compiler then generates the entire reaction network before launching a stochastic reaction-diffusion algorithm.

A different approach is taken by PySB,[47] where model specification is embedded in the programming language Python. A model (or part of a model) is represented as a Python programme. This allows users to store higher-order biochemical processes such as catalysis or polymerisation as macros and re-use them as needed. The models can be simulated and analysed using Python libraries, but PySB models can also be exported into BNGL,[4] kappa,[1] and SBML.[34]

Models involving multi-state and multi-component species can also be specified in Level 3 of the Systems Biology Markup Language (SBML) [34] using the multi package. A draft specification is available,[48] and software support is under development.

Thus, by only considering states and features important for a particular reaction, rule-based model specification eliminates the need to explicitly enumerate every possible molecular state that can undergo a similar reaction, and thereby allows for efficient specification.

The computation problem[edit]

When running simulations on a biological model, any simulation software evaluates a set of rules, starting from a specified set of initial conditions, and usually iterating through a series of time steps until a specified end time. One way to classify simulation algorithms is by looking at the level of analysis at which the rules are applied: they can be population-based, single-particle-based or hybrid.

Population-based rule evaluation[edit]In Population-based rule evaluation, rules are applied to populations. All molecules of the same species in the same state are pooled together. Application of a specific rule reduces or increases the size of one of the pools, possibly at the expense of another.

Some of the best-known classes of simulation approaches in computational biology belong to the population-based family, including those based on the numerical integration of ordinary and partial differential equations and the Gillespie stochastic simulation algorithm.

Differential equations describe changes in molecular concentrations over time in a deterministic manner. Simulations based on differential equations usually do not attempt to solve those equations analytically, but employ a suitable numerical solver.

The stochastic Gillespie algorithm changes the composition of pools of molecules through a progression of randomnessreaction events, the probability of which is computed from reaction rates and from the numbers of molecules, in accordance with the stochastic master equation.[40]

In population-based approaches, one can think of the system being modeled as being in a given state at any given time point, where a state is defined according to the nature and size of the populated pools of molecules. This means that the space of all possible states can become very large. With some simulation methods implementing numerical integration of ordinary and partial differential equations or the Gillespie stochastic algorithm, all possible pools of molecules and the reactions they undergo are defined at the start of the simulation, even if they are empty. Such "generate-first" methods[4]scale poorly with increasing numbers of molecular states.[49] For instance, it has recently been estimated that even for a simple model of CaMKII with just 6 states per subunits and 10 subunits, it would take 290 years to generate the entire reaction network on a 2.54 GHz Intel Xeon processor.[50] In addition, the model generation step in generate-first methods does not necessarily terminate, for instance when the model includes assembly of proteins into complexes of arbitrarily large size, such as actin filaments. In these cases, a termination condition needs to be specified by the user.[3][5]

Even if a large reaction system can be successfully generated, its simulation using population-based rule evaluation can run into computational limits. In a recent study, a powerful computer was shown to be unable to simulate a protein with more than 8 phosphorylation sites (  phosphorylation states) using ordinary differential equations.[14]

Methods have been proposed to reduce the size of the state space. One is to consider only the states adjacent to the present state (i.e. the states that can be reached within the next iteration) at each time point. This eliminates the need for enumerating all possible states at the beginning. Instead, reactions are generated "on-the-fly"[4] at each iteration. These methods are available both for stochastic and deterministic algorithms. These methods still rely on the definition of an (albeit reduced) reaction network - in contrast to the "network-free" methods discussed below.

Even with "on-the-fly" network generation, networks generated for population-based rule evaluation can become quite large, and thus difficult - if not impossible - to handle computationally. An alternative approach is provided by particle-based rule evaluation.

Particle-based rule evaluation[edit]

Figure 2: Principles of particle-based modeling. In particle-based modeling, each particle is tracked individually

through the simulation. At any point, a particle only "sees" the rules that apply to it. This figure follows two

molecular particles (one of type A in red, one of type B in blue) through three steps in a hypothetical simulation

following a simple set of rules (given on the right). At each step, the rules that potentially apply to the particle

under consideration are highlighted in that particle's colour.

In particle-based (sometimes called "agent-based") simulations, proteins, nucleic acids, macromolecular complexes or small molecules are represented as individual software objects, and their progress is tracked through the course of the entire simulation. [51] Because particle-based rule evaluation keeps track of individual particles rather than populations, it comes at a higher computational cost when modeling systems with a high total number of particles, but a small number of kinds (or pools) of particles.[51] In cases of combinatorial complexity, however, the modeling of individual particles is an advantage because, at any given point in the simulation, only existing molecules, their states and the reactions they can undergo need to be considered. Particle-based rule evaluation does not require the generation of complete or partial reaction networks at the start of the simulation or at any other point in the simulation and is therefore called "network-free".

This method reduces the complexity of the model at the simulation stage, and thereby saves time and computational power.[9] A detailed discussion of the computational cost of population-based versus particle-based methods is summarised in a recent study by Hogg et al. [10] The simulation follows each particle, and at each simulation step, a particle only "sees" the reactions (or rules) that apply to it. This depends on the state of the particle and, in some implementation, on the states of its neighbours in a holoenzyme or complex. As the simulation proceeds, the states of particles are updated according to the rules that are fired. Figure 2 illustrates the process of particle-based modeling using a simple system with three molecules of type A and one molecular tetramer of type B, which goes through three simulation steps following a simple set of rules.

Some particle-based simulation packages use an ad-hoc formalism for specification of reactants, parameters and rules. Others can read files in a recognised rule-based specification format such as BNGL.[4]

Non-spatial particle-based methods[edit]StochSim[11][52] is a particle-based stochastic simulator used mainly to model chemical reactions and other molecular transitions. The algorithm used in StochSim is different from the more widely known Gillespie stochastic algorithm[40] in that it operates on individual entities, not entity pools, making it particle-based rather than population-based.

In StochSim, each molecular species can be equipped with a number of binary state flags representing a particular modification. Reactions can be made dependent on a set of state flags set to particular values. In addition, the outcome of a reaction can include a state flag being changed. Moreover, entities can be arranged in geometric arrays (for instance, for holoenzymes consisting of several subunits), and reactions can be "neighbor-sensitive", i.e. the probability of a reaction for a given entity is affected by the value of a state flag on a neighboring entity. These properties make StochSim ideally suited to modeling multi-state molecules arranged in holoenzymes or complexes of specified size. Indeed, StochSim has been used to model clusters of bacterial chemotactic receptors,[53] and CaMKII holoenzymes.[27]

An extension to StochSim has been presented by Colvin et al.[12] Their particle-based simulator DYNSTOC uses a StochSim-like algorithm to simulate models specified in the BioNetGen language (BNGL),[4] which improves the handling of molecules within macromolecular complexes.[12]

Another particle-based stochastic simulator that can read BNGL input files is RuleMonkey. [13] Its simulation algorithm[9]differs from the algorithms underlying both StochSim and DYNSTOC in that the simulation time step is variable.

The Network-Free Stochastic Simulator (NFSim) differs from those described above by allowing for the definition of reaction rates as arbitrary mathematical or conditional expressions and thereby facilitates selective coarse-graining of models.[14]RuleMonkey and NFsim implement distinct but related simulation algorithms. A detailed review and comparison of both tools is given by Yang and Hlavacek.[54]

It is easy to imagine a biological system where some components are complex multi-state molecules, whereas others have few possible states (or even just one) and exist in large numbers. A hybrid approach has been proposed to model such systems: Within the Hybrid Particle/Population (HPP) framework, the user can specify a rule-based model, but can designate some species to be treated as populations (rather than particles) in the subsequent simulation. [10] This method combines the computational advantages of particle-based modeling for multi-state systems with relatively low molecule numbers and of population-based modeling for systems with high molecule numbers and a small number of possible states. Specification of HPP models is supported by BioNetGen, [4] and simulations can be performed with NFSim.[14]

Spatial particle-based methods[edit]

Figure 3: Screenshot from an MCell simulation of calcium signaling within the spine. Although other types of

calcium-regulated molecules were included in the simulations, only CaMKII molecules are visualized. They are

shown in red when bound to calmodulin and in black when unbound. The simulation compartment is a

reconstruction of a dendritic spineas presented by Kinney et al. (J Comp Neurol. 2013).[55] The area of

thepostsynaptic density is shown in red, the spine head and neck in gray, and the parent dendrite in yellow.

The figure was generated by visualizing the simulation results in Blender.

Spatial particle-based methods differ from the methods described above by their explicit representation of space.

One example of a particle-based simulator that allows for a representation of cellular compartments is SRSim.[16][17] SRSim is integrated in the LAMMPS molecular dynamics simulator[56][57] and allows the user to specify the model in BNGL.[4] SRSim allows users to specify the geometry of the particles in the simulation, as well as interaction sites. It is therefore especially good at simulating the assembly and structure of complex biomolecular complexes, as evidenced by a recent model of the inner kinetochore.[58]

MCell[18][19][20][59] allows individual molecules to be traced in arbitrarily complex geometric environments which are defined by the user. This allows for simulations of biomolecules in realistic reconstructions of living cells, including cells with complex geometries like those of neurons. As an illustration, Figure 3 shows a screenshot from a simulation of calcium-regulated proteins. The reaction compartment is a reconstruction of a dendritic spine.[55] Visualizations are supported by a specialized plug-in ("CellBlender") for the open source program Blender.[60]

MCell uses an ad-hoc formalism within MCell itself to specify a multi-state model: In MCell, it is possible to assign "slots" to any molecular species. Each slot stands for a particular modification, and any number of slots can be assigned to a molecule. Each slot can be occupied by a particular state. The states are not necessarily binary. For instance, a slot describing binding of a particular ligand to a protein of interest could take the states "unbound", "partially bound", and "fully bound".

The slot-and-state syntax in MCell can also be used to model multimeric proteins or macromolecular complexes. When used in this way, a slot is a placeholder for a subunit or a molecular component of a complex, and the state of the slot will indicate whether a specific protein component is absent or present in the complex. A way to think about this is that MCell macromolecules can have several dimensions: A "state dimension" and one or more "spatial dimensions". The "state dimension" is used to describe the multiple possible states making up a multi-state protein, while the spatial dimension(s) describe topological relationships between neighboring subunits or members of a macromolecular complex. One drawback of this method for representing protein complexes, compared to Meredys, is that MCell does not allow for the diffusion of complexes, and hence, of multi-state molecules. This can in some cases be circumvented by adjusting the diffusion constants of ligands that interact with the complex, by using checkpointing functions or by combining simulations at different levels.

Examples of multi-state models in biology[edit]

A (by no means exhaustive) selection of models of biological systems involving multi-state molecules and using some of the tools discussed here is give in the table below.

Examples of multi-state models of biological systems

Biological system Specification Computation Reference

Bacterial chemotaxis signalling pathway StochSim StochSim [61]

CaMKII regulation StochSim StochSim [27]

ERBB receptor signalling BioNetGen NFSim [29]

Eukaryotic synthetic gene circuits BioNetGen, PROMOT[62] COPASI   [63]    [30]

RNA signaling Kappa KaSim [64]

Cooperativity of allosteric proteins Allosteric Network Compiler (ANC) MATLAB [6]

Chemosensing in Dictyostelium Simmune Simmune [44]

T-cell receptor activation SSC SSC [65]

Human mitotic kinetochore BioNetGen SRSim [66]

Cell cycle of fission yeast ML-Rules JAMES II[42] [41]

What are biomolecules? 4 Different Types of BiomoleculesWHAT ARE BIOLMOLECULES

Biomolecules are those substance which are present exclusively in the living organisms.

They are formed in the body to manage the needs of physiology and growth.

There are many biomolecules in nature and one can read them in detail inbiochemistry.Biochemistry describes their formation, physiological role and any deficiency diseases.The biomolecules are present in the body of humans, animals and plants.

Their primary formation from the basic elements seems to occur in plants.

Once formed, these molecules then pass on to animals through the food chain.

If you wish to directly go through list of biomolecules, you can refer to table at the bottom of the article.

DIFFERENT TYPES OF BIOMOLECULES:

Biomolecules are of different types and can be classified as

1. Based on availability or source.2. Based on their role or purpose in body.3. Based on their chemistry.

Based on availability: Different types of biomolecules are available in different set of organisms. Not all the bio-molecules of plants are available in animals and vice-verse.Hence based on the availability they can be divided as those available in

1. plants2. animals3. Microbes.

Example: Lignin, chitin are biomolecules present only in plants in plant cell wall. While the same cell wall in bacteria is made of  gluco-polysacharrides gluco-peptides are present in bacterial cell wall. While animals do not have a cell wall. Hence there is difference of existence of biomolecules.

Besides these plants have alkaloids, glycosides, tannins, resins, gums etc. which are specific to them.In animals biomolecules like epinephrine, dopamine like substances are so specific.

Based on purpose: Further these bio-molecules have different role and purpose in body. So their existence in this manner is solely dependent on the purpose.Ex: Hemoglobin is a protein molecule formed in combination with iron (heme). It is  meant for oxygen supply in the body. It is available only in animals and humans. But not available and also not needed for plants and microbes.

Though there are many biomolecules based on their role in body. Based on their role in the body. There are 4 types of bio-molecules as.

1. Food sources.2. Body elements3. Primary metabolites4. Secondary metabolites.

Food sources: These are the substances which act as food materials. They give energy and nutrients to all the living beings on the earth.Examples include: Carbohydrates, proteins, fats, vitamins.Constitutional (Form Body) : These are the molecules which make up the body structure. They also tend to control the body physiology.Examples include: DNA, RNA, steroids, cholesterol etc. DNA forms the genes and also mRNA, RNA from the body proteins. Steroids are part of many hormones.

Primary metabolites: These are the substances which act as intermediates in the body metabolism and other reactions. They are formed from one or other bio-molecules like food based or constitutional based.Ex: UDP-Glucuronic acid, keto-glutaric acid etc.

Secondary metabolites: These are mostly end metabolic substances. They are mostly excreted from the body.Ex: Urea, uric acid, ketones etc.

Biomolecules are the natural substance present from birth to death of living being. They are synthesized in the body by use of different elements from nature. Substances like carbon-dioxide, ammonium, water and other inorganic elements from soil contribute to the chemical formation of these molecules.

LIST OF BIOMOLECULES:

In a simple worksheet explaining characters, role and availability.

Biomolecule Class Characters Presenc

e

Glucose Carbohydrates. Sweet in taste & provides energy to body

Animals & plants

Sucrose (sugar)

Sweet in taste & provides energy to body

Animals & Plants

Starch Breaks down to sugars Animals & plants

Cellulose Breaks down to sugars & eaten by animals

Plants

DNA Nucleic Acid Regulates Body composition & Physiology

Animals & Plants

RNA Nucleic Acid Protein synthesis & physiology

Animals & Plants

Amino acids Proteins To make up proteins and body building

Animals & plants

Enzymes Proteins As catalysts to aid reactions

Animals & plants

Hormones Amides, lipids, amines Act as messengers to regulate physiology

Animals & plants

Gums Carbohydrates in nature

Plants

Glycosides Made of carbohydrate Metabolites but are Plants

Biomolecule Class Characters Presenc

e

+ Glycoside moiety used in medicine

Tannins Metabolites Waste matter for plants but used by humans

Plants

Cholesterol Lipids Forms cell membrane Animals

Essential oils

Hydrocarbons (volatile oil which are gases   at high temperature.

As metabolites. To attract insects for pollination. Humans use as perfumes.

Plants

Vitamins A,B,C,D,E & K

Vitamins To aid in body physiology

Animals & Plants

This is not the end of the list but a brief categorization of biomolecules.

But of all those available, only 4 important biomolecules are studied widely.

These 4 major biomolecules include

1. Carbohydrates.2. Proteins (amino-acids)3. Fats4. Nucleic acids (DNA, RNA, nucleotides).

These are studied so because of their role in health and diseases.

IMPORTANCE OF BIOMOLECULES:

Biomolecules are used for different purposes like food, medicine, cosmetics etc. by humans. Below are few uses of them

1. Carbohydrates , proteins, fats are used as food stuffs in various forms.2. Volatile oils or essential oils are used for perfumes.3. Compounds like alkaloids, glycosides, tannins are used in medicine.

4. Tannins are also used to tan (toughen) the leather in industry.These biomolecules are vital to the living beings. But they can be harmful and toxic if misused or over stagnated in the body.

Biomolecules 

Although there is vast diversity of living organisms. The chemical compositon and metabolic reactions of the organisms appear to be similar. The composition of living tissues and non-living matter also appear to be similar in qualitative analysis.Closer analysis reveals that the relative abundance of carbon, hydrogen and oxygen is higher in living system.

All forms of life are composed of biomolecules only. Biomolecules are organic molecules especially macromolecules like carbohydrates, proteins in living organisms. All living forms bacteria, algae, plant and animals are made of similar macromolecules that are responsible for life. All the carbon compounds we get from living tissues can be called biomolecules.

 

Biomolecules DefinitionBack to Top

Biomolecules are molecules that occur naturally in living organisms. Biomolecules include macromolecules like proteins, carbohydrates, lipids and nucleic acids. It also includes small molecules like primary and secondary metabolites and natural products. Biomolecules consists mainly of carbon and hydrogen with nitrogen, oxygen, sulphur, and phosphorus. Biomolecules are very large molecules of many atoms, that are covalently bound together.

Classes of BiomoleculesBack to Top

There are four major classes of biomolecules: 

Carbohydrates Lipids Proteins Nucleic acids

Carbohydrates

Carbohydrates are good source of energy. Carbohydrates (polysaccharides) are long chains of sugars. Monosaccharides are simple sugars that are composed of 3-7 carbon atoms. They have a free aldehyde or ketone group, which acts as reducing agents and are known as reducing sugars. Disaccharides are made of  two monosaccharides. The bonds shared between two monosaccharides is the glycosidic bonds. Monosaccharides and disaccharides are sweet, crystalline and water soluble substances.Polysaccharides are polymers of monosaccharides. They are unsweet, and complex carbohydrates.They are insoluble in water and are not in crystalline form. 

Example: glucose, fructose, sucrose, maltose, starch, cellulose etc.

Lipids

Lipids are composed of long hydrocarbon chains. Lipid molecules hold a large amount of energy and are energy storage molecules. Lipids are generally esters of fatty acids and are building blocks of biological membranes. Most of the lipids have a polar head and non-polar tail. Fatty acids can be unsaturated and saturated fatty acids. 

Lipids present in biological membranes are of three classes based on the type of hydrophilic head present:

Glycolipids are lipids whose head contains oligosaccharides with 1-15 saccharide residues.   Phospholipids contain a positively charged head which are linked to the negatively charged

phosphate groups.  Sterols, whose head contain a steroid ring. Example steroid.

Example of lipids: oils, fats, phospholipids, glycolipids, etc.

Proteins

Proteins are heteropolymers of stings of amino acids. Amino acids are joined together by the peptide bond which is formed in between the carboxyl group and amino group of successive amino acids. Proteins are formed from 20 different amino acids, depending on the number of amino acids and the sequence of amino acids. 

There are four levels of protein structure:

Primary structure of Protein - Here protein exist as long chain of amino acids arranged in a particular sequence. They are non-functional proteins.

Secondary structure of protein - The long chain of proteins are folded and arranged in a helix shape, where the amino acids interact by the formation of hydrogen bonds. This structure is called the pleated sheet. Example: silk fibres. 

Tertiary structure of protein - Long polypeptide chains become more stabilizes by folding and coiling, by the formation of ionic or hydrophobic bonds or disulphide bridges, this results in the tertiary structure of protein.

Quaternary  structure of protein - When a protein is an assembly of more than one polypeptide or subunits of its own, this is said to be the quaternary structureof protein. Example: Haemoglobin, insulin. 

Nucleic Acids

Nucleic acids are organic compounds with heterocyclic rings. Nucleic acids are made of polymer of nucleotides. Nucleotides consists of nitrogenous base, a pentose sugar and a phosphate group. A nucleoside is made of nitrogenous base attached to a pentose sugar. The nitrogenous bases are adenine, guanine, thyamine, cytosine and uracil. Polymerized nucleotides form DNA and RNA which are genetic material. 

Functions of BiomoleculesBack to Top

Carbohydrates provide the body with source of fuel and energy, it aids in proper functioning of our brain, heart and nervous, digestive and immune system. Deficiency of carbohydrates in the diet causes fatigue, poor mental function. 

Each protein in the body has specific functions, some proteins provide structural support, help in body movement, and also defense against germs and infections. Proteins can be antibodies, hormonal, enzymes and contractile proteins.

Lipids, the primary purpose of lipids in body is energy storage. Structural membranes are composed of lipids which forms a barrier and controls flow of material in and out of the cell. Lipid hormones, like sterols, help in mediating communication between cells. 

Nucleic Acids are the DNA and RNA, they carry genetic information in the cell. They also help in synthesis of proteins, through the process of translation and transcription.

Structure of BiomoleculesBack to Top

Structure of biomolecule is intricate folded, three-dimensional structure that is formed by protein, RNA, and DNA. The structure of these molecules are in different forms, primary, secondary, tertiary and quaternary structure. The scaffold for this is provided by the hydrogen bonds within the molecule.

Primary structure of a biomolecule is the exact specification of its atomic composition and and the chemical bonds connecting the atoms. 

Secondary structure of the biomolecule is the three-dimensional form of biopolymers, secondary structure is defined by the hydrogen bonds of the biomolecules. 

Tertiary structure of the biomolecule is the three-dimensional structure,defined by its atomic coordinates, by the formation of hydrogen, ionic or sulphide bonds. 

Quaternary structure is the arrangement of multiple folds of complex, in a mutli-subunit complex. 

Biomolecules - Definition, Types, Structure, Properties and Its applications

Definition of Biomolecule: 

An organic compound normally present as an essential component of living organism.

 Characteristics of Biomolecules:

1) Most of them are organic compounds. 2) They have specific shapes and dimensions. 3) Functional group determines their chemical properties. 4) Many of them arc asymmetric. 5) Macromolecules are large molecules and are constructed from small building block molecules. 6) Building block molecules have simple structure. 7) Biomolecules first gorse by chemical evolution.

Important Biomolecules of life:

1) Water: Being the universal solvent and major constituents (60%) of any living body without which life is impossible. It acts as a media for the physiological and biochemical reactions in the body itself. Maintain the body in the required turgid condition.

2) Carbohydrates: It is very important for source of energy for any physical body function.

3) Proteins: These are very important from body maintenance point of view,helps in tissue, cell formation.

4) Lipids: These are very important from energy source as well as human nutrition point of view.

5) Nucleic Acids: Nucleic acids are very important as DNA carries the hereditary information and RNA helps in protein formation for the body. 6) Enzymes: Enzymes are simple or combined proteins acting as specific catalysts and activates the various biochemical and metabolic processes within the body.

Table: Fundamental Biological Molecules (Biomolecules):

Sr. No. Small Molecule Atomic Constituents Derived Macro - Molecule1 Amino Acid C, H, O, N (S) Proteins2 Sugars C, H, O Starch, Glycogen3 Fatty Acids C, H, O Fats, Oils

4Purines and Pyrimidine C, H, O, N Nucleic Acids

5 Nucleotide C, H, O, N, P Nucleic Acids (DNA and RNA)