Biomolecular engineering
Biomolecular engineering is the application of engineering principles and practices to the purposeful manipulation of molecules of biological origin. Biomolecular engineers integrate knowledge of
Biomolecular engineers purposefully manipulate
Timeline
History
During World War II,
Future
Bio-inspired technologies of the future can help explain biomolecular engineering. Looking at the
Basic biomolecules
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
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
Carbohydrates
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.
Nucleic acids
Lipids
Of molecules
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. Recombinant DNA is used for a wide range of applications.
Method
The traditional method for creating recombinant DNA typically involves the use of
Advances in
Applications
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
Site-directed mutagenesis
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
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.
Applications
Site-directed mutagenesis can be helpful for many different reasons. A single base-pair replacement will change the
Bio-immobilization and bio-conjugation
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 a bioreactor. 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
The
Biomolecular engineering techniques involved in PCR
A number of biomolecular engineering strategies have played a very important role in the development and practice of
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)
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 of ELISA 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, these antigens 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.
Techniques involved in ELISA
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
In industry
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
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, insulin produced 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
P/V α Ni3di3
where di= crystallizer impeller diameter
Ni= impeller rotation rate
Related industries
Bioengineering
A broad term encompassing all engineering applied to the life sciences. This field of study utilizes the principles of biology along 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.
- pharmaceuticals.
- Industrial microbiology - The implementation of microorganisms in the production of industrial products such as food and antibiotics. Another common application of industrial microbiology is the treatment of wastewater in chemical plants via utilization of certain microorganisms.
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
- Biocatalysis – Chemical transformations using enzymes.
- Bioseparations – Separation of biologically active molecules.
- Kinetics (chemistry)– Analysis of reactions involving cell growth and biochemicals.
- Bioreactor design and analysis – Design of reactors for performing biochemical transformations.
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
Bioelectrical engineering involves the electrical fields generated by living cells or organisms. Examples include the
- Bioelectrochemistry - Chemistry concerned with electron/proton transport throughout the cell
- Bioelectronics - Field of research coupling biology and electronics
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
- 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 disabled people
- 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
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
Newly developed and offered undergraduate programs across the United States, often coupled to the chemical engineering program, allow students to achieve a
See also
- Biomimetics
- Biopharmaceuticals
- Bioprocess engineering
- List of biomolecules
- Molecular engineering
References
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- ^ Braconi, C.; Huang, N.; Patel, T. (2010). "MicroRNA-Dependent Regulation of DNA Methyltransferase-1 in Human Malignant Cholangiocytes. Hepatology." Hepatology. ppg 881-890.
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- ^ Organization for Economic Co-Operation and Development. Key Biotechnology Indicators: Biotechnology Applications. http://www.oecd.org/document/30/0,3746,en_2649_34451_40146462_1_1_1_1,00.html (accessed April 10, 2012).
- ^ Mendelsohn, Jens-Peter. "Biotechnology Plant for Insulin Production" (PDF). Archived from the original (PDF) on June 12, 2013. Retrieved April 12, 2012.
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- ^ Auyang, Sunny, Y. "Why chemical engineering emerged in America instead of Germany". Eidgenossische Technische Hochschule. Retrieved April 11, 2012.
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- ^ "Bachelor of Science BioMolecular Engineering". Milwaukee School of Engineering. Archived from the original on 2012-04-20. Retrieved 2012-04-11.
Further reading
- Biomolecular engineering at interfaces (article)
- Recent Progress in Biomolecular Engineering
- Biomolecular sensors ISBN 074840791X(alk. paper)