Molecular biology /məˈlɛkjʊlər/ is a branch of biology that concerns the molecular basis of biological activity between biomolecules in the various systems of a cell, including the interactions between DNA, RNA, proteins and their biosynthesis, as well as the regulation of these interactions. Writing in Nature in 1961, William Astbury described 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.
Researchers in molecular biology use specific techniques native to molecular biology but increasingly combine these with techniques and ideas from genetics and biochemistry. There is not a defined line between these disciplines. This is shown in the following schematic that depicts one possible view of the relationships between the fields:
Much of molecular biology is quantitative, and recently much work has been done at its interface with computer science in bioinformatics and computational biology. In the early 2000s, the study of gene structure and function, molecular genetics, has been among the most prominent sub-fields of molecular biology. Increasingly many other areas of biology focus on molecules, either directly studying interactions in their own right such as in cell biology and developmental biology, or indirectly, where molecular techniques are used to infer historical attributes of populations or species, as in fields in evolutionary biology such as population genetics and phylogenetics. There is also a long tradition of studying biomolecules "from the ground up" in biophysics.
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 polymerase chain reaction (PCR), and/or restriction enzymes into a plasmid (expression vector). A vector has 3 distinctive features: an origin of replication, a multiple cloning site (MCS), and a selective marker usually antibiotic resistance. Located upstream of the multiple cloning site are the promoter regions and the transcription start site which regulate the expression of cloned gene. This plasmid can be inserted into either bacterial or animal cells. Introducing DNA into bacterial cells can be done by transformation 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. The plasmid may be integrated into the genome, resulting in a stable transfection, or may remain independent of the genome, called transient transfection.
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) 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 one DNA molecule to become 1.07 billion molecules in less than two hours. The PCR technique can be used to introduce restriction enzyme sites to ends of DNA molecules, or to mutate 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 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.
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.
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. 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 transgene copy number in transgenic mice or in the engineering of gene knockout embryonic stem cell lines.
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 labeled complement 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.
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. 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.
The eastern blotting technique is used to detect post-translational modification of proteins. Proteins blotted on to the PVDF or nitrocellulose membrane are probed for modifications using specific substrates.
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 fragments. 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. 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 complementary DNA (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. 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.
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.
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.
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.
Clinical research and medical therapies arising from molecular biology are partly covered under gene therapy. 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, and regulations of various parts of cells which can be used to efficiently target new drugs, diagnosis disease, and understand the physiology of the cell.
Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms. Biochemical processes give rise to the complexity of life.
A sub-discipline of both biology and chemistry, biochemistry can be divided in three fields; molecular genetics, protein science and metabolism. Over the last decades of the 20th century, biochemistry has through these three disciplines become successful at explaining living processes. Almost all areas of the life sciences are being uncovered and developed by biochemical methodology and research. Biochemistry focuses on understanding how biological molecules give rise to the processes that occur within living cells and between cells, which in turn relates greatly to the study and understanding of tissues, organs, and organism structure and function.Biochemistry is closely related to molecular biology, the study of the molecular mechanisms by which genetic information encoded in DNA is able to result in the processes of life.Much of biochemistry deals with the structures, functions and interactions of biological macromolecules, such as proteins, nucleic acids, carbohydrates and lipids, which provide the structure of cells and perform many of the functions associated with life. The chemistry of the cell also depends on the reactions of smaller molecules and ions. These can be inorganic, for example water and metal ions, or organic, for example the amino acids, which are used to synthesize proteins. The mechanisms by which cells harness energy from their environment via chemical reactions are known as metabolism. The findings of biochemistry are applied primarily in medicine, nutrition, and agriculture. In medicine, biochemists investigate the causes and cures of diseases. In nutrition, they study how to maintain health wellness and study the effects of nutritional deficiencies. In agriculture, biochemists investigate soil and fertilizers, and try to discover ways to improve crop cultivation, crop storage and pest control.Biophysics
Biophysics is an interdisciplinary science that applies approaches and methods traditionally used in physics to study biological phenomena. Biophysics covers all scales of biological organization, from molecular to organismic and populations. Biophysical research shares significant overlap with biochemistry, molecular biology, physical chemistry, physiology, nanotechnology, bioengineering, computational biology, biomechanics, developmental biology and systems biology.
The term biophysics was originally introduced by Karl Pearson in 1892. Ambiguously, the term biophysics is also regularly used in academia to indicate the study of the physical quantities (e.g. electric current, temperature, stress, entropy) in biological systems, which is, by definition, performed by physiology. Nevertheless, other biological sciences also perform research on the biophysical properties of living organisms including molecular biology, cell biology, biophysics, and biochemistry.Central dogma of molecular biology
The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It is often stated as "DNA makes RNA and RNA makes protein," although this is not its original meaning. It was first stated by Francis Crick in 1957, then published in 1958:
and re-stated in a Nature paper published in 1970:
A second version of the central dogma is popular but incorrect. This is the simplistic DNA → RNA → protein pathway published by James Watson in the first edition of The Molecular Biology of the Gene (1965). Watson's version differs from Crick's because Watson describes a two-step (DNA → RNA and RNA → protein) process as the central dogma. While the dogma, as originally stated by Crick, remains valid today, Watson's version does not.
The dogma is a framework for understanding the transfer of sequence information between information-carrying biopolymers, in the most common or general case, in living organisms. There are 3 major classes of such biopolymers: DNA and RNA (both nucleic acids), and protein. There are 3×3=9 conceivable direct transfers of information that can occur between these. The dogma classes these into 3 groups of 3: three general transfers (believed to occur normally in most cells), three special transfers (known to occur, but only under specific conditions in case of some viruses or in a laboratory), and three unknown transfers (believed never to occur). The general transfers describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA information can be copied into mRNA (transcription), and proteins can be synthesized using the information in mRNA as a template (translation). The special transfers describe: RNA being copied from RNA (RNA replication), DNA being synthesised using an RNA template (reverse transcription), and proteins being synthesised directly from a DNA template without the use of mRNA. The unknown transfers describe: a protein being copied from a protein, synthesis of RNA using the primary structure of a protein as a template, and DNA synthesis using the primary structure of a protein as a template - these are not thought to naturally occur.Eric F. Wieschaus
Eric Francis Wieschaus (born June 8, 1947 in South Bend, Indiana) is an American evolutionary developmental biologist and 1995 Nobel Prize-winner.
Born in South Bend, Indiana, he attended John Carroll Catholic High School in Birmingham, AL before attending the University of Notre Dame for his undergraduate studies (B.S., biology), and Yale University (Ph.D., biology) for his graduate work. In 1978, he moved to his first independent job, at the European Molecular Biology Laboratory in Heidelberg, Germany and moved from Heidelberg to Princeton University in the United States in 1981.Much of his research has focused on embryogenesis in the fruit fly Drosophila melanogaster, specifically in the patterning that occurs in the early Drosophila embryo. Most of the gene products used by the embryo at these stages are already present in the unfertilized egg and were produced by maternal transcription during oogenesis. A small number of gene products, however, are supplied by transcription in the embryo itself. He has focused on these "zygotically" active genes because he believes the temporal and spatial pattern of their transcription may provide the triggers controlling the normal sequence of embryonic development. Saturation of all the possible mutations on each chromosome by random events to test embryonic lethality was done by Eric Wieschaus.In 1995, he was awarded the Nobel Prize in Physiology or Medicine with Edward B. Lewis and Christiane Nüsslein-Volhard as co-recipients, for their work revealing the genetic control of embryonic development.As of 2018, Wieschaus is the Squibb Professor in Molecular Biology at Princeton. He was formerly Adjunct Professor of Biochemistry at the University of Medicine and Dentistry of New Jersey – Robert Wood Johnson Medical School.
He has three daughters and is married to molecular biologist Gertrud Schüpbach, who is also a professor of Molecular Biology at Princeton University, working on Drosophila oogenesis. He is an atheist and is one of the seventy seven Nobel Laureates who signed the petition to repeal the Louisiana Science Education Act.European Molecular Biology Laboratory
The European Molecular Biology Laboratory (EMBL) is a molecular biology research institution supported by 25 member states, four prospect and two associate member states. EMBL was created in 1974 and is an intergovernmental organisation funded by public research money from its member states. Research at EMBL is conducted by approximately 85 independent groups covering the spectrum of molecular biology. The list of independent groups at EMBL or any other research institute in Molecular Biology in Europe can be found at http://www.europe-bio.com. The Laboratory operates from six sites: the main laboratory in Heidelberg, and outstations in Hinxton (the European Bioinformatics Institute (EBI), in England), Grenoble (France), Hamburg (Germany), Monterotondo (near Rome) and Barcelona (Spain). EMBL groups and laboratories perform basic research in molecular biology and molecular medicine as well as training for scientists, students and visitors. The organization aids in the development of services, new instruments and methods, and technology in its member states.
Israel is the only full member state located outside EuropeEuropean Molecular Biology Organization
The European Molecular Biology Organization (EMBO) is a professional organization of more than 1,800 life scientists. Its goal is to promote research in life science and enable international exchange between scientists. It organizes courses, workshops and conferences, publishes five scientific journals and supports individual scientists and projects. The organization was founded in 1964 and is a founding member of the Initiative for Science in Europe. As of 2016 the Director of EMBO is Maria Leptin, a developmental biologist at the University of Cologne, Germany.IntEnz
IntEnz (Integrated relational Enzyme database) contains data on enzymes organized by enzyme EC number and is the official version of the Enzyme Nomenclature system developed by the International Union of Biochemistry and Molecular Biology.Intelligent Systems for Molecular Biology
Intelligent Systems for Molecular Biology (ISMB) is an annual academic conference on the subjects of bioinformatics and computational biology organised by the International Society for Computational Biology (ISCB). The principal focus of the conference is on the development and application of advanced computational methods for biological problems. The conference has been held every year since 1993 and has grown to become one of the largest and most prestigious meetings in these fields, hosting over 2,000 delegates in 2004. From the first meeting, ISMB has been held in locations worldwide; since 2007, meetings have been located in Europe and North America in alternating years. Since 2004, European meetings have been held jointly with the European Conference on Computational Biology (ECCB).
The main ISMB conference is usually held over three days and consists of presentations, poster sessions and keynote talks. Most presentations are given in multiple parallel tracks; however, keynote talks are presented in a single track and are chosen to reflect outstanding research in bioinformatics. Notable ISMB keynote speakers have included eight Nobel laureates. The recipients of the ISCB Overton Prize and ISCB Accomplishment by a Senior Scientist Award are invited to give keynote talks as part of the programme. The proceedings of the conference are currently published by the journal Bioinformatics.International Union of Biochemistry and Molecular Biology
The International Union of Biochemistry and Molecular Biology (IUBMB) is an international non-governmental organisation concerned with biochemistry and molecular biology. Formed in 1955 as the International Union of Biochemistry, the union has presently 77 member countries (as of 2008).IUBMB organizes a triennial Congress of Biochemistry and Molecular Biology, and sponsors more frequent conferences, symposia, educational activities and lectures.
It publishes standards on biochemical nomenclature, including enzyme nomenclature, in some cases jointly with the International Union of Pure and Applied Chemistry (IUPAC).
IUBMB has instituted the Wood Whelan Research fellowship scheme for budding researchers. It is considered as a prestigious award for doctoral students. Candidates are selected based on a competitive project proposal and reference letters. The award scheme provides opportunity to work on a specified project in a different laboratory in a foreign country.
It is associated with the journals Biochemistry and Molecular Biology Education (formerly Biochemical Education), BioEssays, BioFactors, Biotechnology and Applied Biochemistry, IUBMB Life, Molecular Aspects of Medicine and Trends in Biochemical Sciences.Intracellular
In cell biology, molecular biology and related fields, the word intracellular means "inside the cell".It is used in contrast to extracellular (outside the cell). The cell membrane (and, in many organisms, the cell wall) is the barrier between the two, and chemical composition of intra- and extracellular milieu (Milieu intérieur) can be radically different. In most organisms, for example, a Na+/K+ ATPase maintains a high potassium level inside cells while keeping sodium low, leading to chemical excitability.Laboratory of Molecular Biology
The Medical Research Council (MRC) Laboratory of Molecular Biology (LMB) is a research institute in Cambridge, England, involved in the revolution in molecular biology which occurred in the 1950–60s. Since then it has remained a major medical research laboratory with a much broader focus. A new £212m replacement building constructed close by to the original site on the Cambridge Biomedical Campus was opened in May 2013. The road outside the new building is named Francis Crick Avenue after the 1962 joint Nobel Prize winner, who co-discovered the helical structure of DNA in 1953.Molecular Biology and Evolution
Molecular Biology and Evolution is a monthly peer-reviewed scientific journal published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. It publishes work in the intersection of molecular biology and evolutionary biology. The founding editors-in-chief were Walter Fitch and Masatoshi Nei; the present editor-in-chief is Sudhir Kumar.
According to the Journal Citation Reports, the journal has a 2017 Impact Factor of 10.217.Natriuretic peptide
A natriuretic peptide is a peptide which induces natriuresis- the excretion of sodium by the kidneys.
Known natriuretic peptides include:
Atrial natriuretic peptide, also known as ANP
Brain natriuretic peptide, also known as BNP
C-type natriuretic peptide, also known as CNP
Dendroaspis natriuretic peptide, also known as DNP
UrodilatinNucleic acid hybridization
In molecular biology, hybridization (or hybridisation) is a phenomenon in which single-stranded deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) molecules anneal to complementary DNA or RNA. Though a double-stranded DNA sequence is generally stable under physiological conditions, changing these conditions in the laboratory (generally by raising the surrounding temperature) will cause the molecules to separate into single strands. These strands are complementary to each other but may also be complementary to other sequences present in their surroundings. Lowering the surrounding temperature allows the single-stranded molecules to anneal or “hybridize” to each other.
DNA replication and transcription of DNA into RNA both rely upon nucleotide hybridization, as do molecular biology techniques including Southern blots and Northern blots, the polymerase chain reaction (PCR), and most approaches to DNA sequencing.Primer (molecular biology)
A primer is a short single-stranded nucleic acid utilized by all living organisms in the initiation of DNA synthesis. The enzymes responsible for DNA replication, DNA polymerases, are only capable of adding nucleotides to the 3’-end of an existing nucleic acid, requiring a primer be bound to the template before DNA polymerase can begin a complementary strand. Living organisms use solely RNA primers, while laboratory techniques in biochemistry and molecular biology that require in vitro DNA synthesis (such as DNA sequencing and polymerase chain reaction) usually use DNA primers, since they are more temperature stable.Protein superfamily
A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similarity is evident. Sequence homology can then be deduced even if not apparent (due to low sequence similarity). Superfamilies typically contain several protein families which show sequence similarity within each family. The term protein clan is commonly used for protease and glycosyl hydrolases superfamilies based on the MEROPS and CAZy classification systems.Sense (molecular biology)
In molecular biology and genetics, the sense of nucleic acid molecules (often DNA or RNA) is the nature of their roles and their complementary molecules' nucleic acid units' roles in specifying amino acids. Depending on the context within molecular biology, sense may have slightly different meanings.Structural biology
Structural biology is a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules (especially proteins, made up of amino acids, and RNA or DNA, made up of nucleotides), how they acquire the structures they have, and how alterations in their structures affect their function. This subject is of great interest to biologists because macromolecules carry out most of the functions of cells, and it is only by coiling into specific three-dimensional shapes that they are able to perform these functions. This architecture, the "tertiary structure" of molecules, depends in a complicated way on each molecule's basic composition, or "primary structure."
Biomolecules are too small to see in detail even with the most advanced light microscopes. The methods that structural biologists use to determine their structures generally involve measurements on vast numbers of identical molecules at the same time. These methods include:
Nuclear magnetic resonance spectroscopy of proteins (NMR)
Electron paramagnetic resonance (EPR)
Cryo-electron microscopy (cryo-EM)
Multiangle light scattering
Small angle scattering
Ultrafast laser spectroscopy
Dual-polarization interferometry and circular dichroismMost often researchers use them to study the "native states" of macromolecules. But variations on these methods are also used to watch nascent or denatured molecules assume or reassume their native states. See protein folding.
A third approach that structural biologists take to understanding structure is bioinformatics to look for patterns among the diverse sequences that give rise to particular shapes. Researchers often can deduce aspects of the structure of integral membrane proteins based on the membrane topology predicted by hydrophobicity analysis. See protein structure prediction.
In the past few years it has become possible for highly accurate physical molecular models to complement the in silico study of biological structures. Examples of these models can be found in the Protein Data Bank.Sydney Brenner
Sydney Brenner (13 January 1927 – 5 April 2019) was a South African biologist. In 2002, he shared the Nobel Prize in Physiology or Medicine with H. Robert Horvitz and Sir John E. Sulston. Brenner made significant contributions to work on the genetic code, and other areas of molecular biology while working in the Medical Research Council (MRC) Laboratory of Molecular Biology in Cambridge, England. He established the roundworm Caenorhabditis elegans as a model organism for the investigation of developmental biology, and founded the Molecular Sciences Institute in Berkeley, California, United States.