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Chemical tools for biological applications

The boundaries between traditional scientific disciplines are becoming less and less distinct. Interdisciplinary cooperation is often required to study complex processes and biomolecular issues. Interdisciplinary cooperation is central to chemical biology, a scientific discipline that applies chemical substances, methods and tools to the study of biological systems ranging from the chemical synthesis of biologically active substances to the specific chemical modification of biomolecules.

The holistic approach of chemical biology gives rise to new approaches for manipulating and studying biological processes at the chemical level in the field of basic research. Chemical biology studies often involve low-molecular weight compounds, so-called “small molecules”, that have been designed using synthetic chemistry methods and tools or identified via biochemical and cell-based screening of large molecule databases.

These molecular tools can have a variety of effects on cells and proteins; for example, they can bind specifically to active proteins and thus show what they do, alter the chemical properties of a protein or visualise its location in the cell. Small molecules can be used in vitro and in vivo, and are primarily characterised by their rapid and often reversible effect, which makes the lengthy preparation of RNAi and other molecules or the genetic manipulation of cells superfluous (see article entitled “Chemical tools for exploring cell division”). 

Pharmaceutical companies are of course extremely interested in functional molecules of this kind. A compound that basic researchers have identified as an inhibitor of a certain cell division protein could have the potential to be used as a cancer drug when the protein in question turns out to be involved in tumorigenesis. The discipline is therefore also of huge economic importance.

Made-to-measure protein building blocks

The combination of methods used in chemistry and biology has already become routine in numerous life sciences areas. © University of Konstanz

So-called non-natural or artificial amino acids are also popular chemical biology tools. In contrast to the 20 canonical amino acids that are the building blocks for the ribosomal biosynthesis of proteins of virtually all organisms, non-natural amino acids are synthesised in the laboratory rather than found in nature. They can be equipped with specific chemical functions, including fluorescent labels or functional side chains that can be used to connect them to other molecules. They are therefore a kind of universal protein-engineering tool that can be used to change or improve the existing properties of a protein or add completely new functions (see article entitled “Marina Rubini – a passionate researcher into protein folding and design”).  

Most artificial amino acids are produced with bacteria. However, as there are no natural base triplets that code for non-natural amino acids, the bacteria's genetic code must first be expanded so that the bacteria can use them as part of their natural protein biosynthesis processes. This can be achieved by specifically suppressing a stop codon in the mRNA, so that a stop codon base triplet leads to the incorporation of a specific amino acid rather than terminates the translation process, which is what it normally does.

To do this, the bacteria also need: 1) specific transfer RNAs (tRNAs) that mediate the integration of a specific non-canonical amino acid into the growing amino acid chain at the ribosome and 2) specific aminoacyl tRNA synthetases that load the tRNAs with non-canonical amino acids. The introduction of specific DNA sequence mutations in the DNA creates stop codons at defined sites of the sequence, thus enabling the site-specific incorporation of a non-canonical amino acid (see article entitled “Red light to elucidate the regulatory mechanisms of gene expression”). 

Targeted enzyme design creates new tools for application in biotechnology

Interdisciplinary study and research programmes give students training beyond rigid disciplinary borders. © University of Konstanz

Enzymes have become integral constituents of many laboratory applications and biotechnological methods because they catalyse specific chemical reactions in biological systems and in test tubes. Standard molecular biology methods such as PCR (polymerase chain reaction), cloning or the production of recombinant proteins are just three examples of the wide range of potential applications. 

Theoretical application possibilities are extremely varied, but in the past they tended to be limited by the natural variation of enzymes, which only work under the right environmental conditions, e.g. at a specific temperature or for a specific substrate. 

“Nature has not evolved polymerases for modern molecular diagnostics applications,” says Andreas Marx, professor of organic chemistry/cellular chemistry and coordinator of the Graduate School Chemical Biology at the University of Konstanz (see article entitled “Andreas Marx – “Chemical Biology” of DNA polymerases”).

However, the combination of molecular biology and chemistry tools has now made it possible to develop new enzymes with new functions in the laboratory. Mutagenesis, selection and molecular modelling make it possible to develop new enzymes for novel applications that facilitate complex synthesis processes in the laboratory, to name but one example (see article entitled “From structure to mechanism”).  

Interdisciplinary study programmes for next-generation researchers

This new scientific orientation is not only seen in research, but is also increasingly a feature of university education. Some universities in Baden-Württemberg are already offering specialised bachelor’s and master’s degrees such as the “Chemical Biology” degree programme at the Karlsruhe Institute of Technology (KIT) or the “Life Sciences” degree programme at the University of Konstanz. Chemical biology plays a particularly important role at Konstanz where a graduate school for doctoral students has been established along with a new research building for chemical biology-related research groups (see articles entitled “New chemical biology centre opened in Konstanz” and "Interdisciplinarity starts with support and supervision"). 

Glossary

  • Desoxyribonucleic acid (DNA) is a double-stranded, helical macromolecule encoding the genetic information of an organism.
  • Enzymes are catalysts in the living cells. They allow the execution of chemical transformations of the metabolism at body temperature.
  • The life sciences involve the research, development, and marketing of products, technologies, and services on the basis of modern biotechnology.
  • PCR or Polymerase Chain Reaction is a biomolecular method to amplify short DNA fragments in an easy way. Therefore, merely the DNA template, an enzyme named DNA polymerase which catalyses the amplification, short complementary oligonucleotides, which serve as starting point for the polymerase and the components of the DNA, which are called desoxynucleosidtriphosphates are needed. The amplification is controlled by several cycles of temperature changes.
  • Ribonucleic acid (abbr. RNA) is a normally single-stranded nucleic acid, which is very similar to DNA. It also consists of a sugar-phosphate backbone and a sequence of four bases. However, the sugar is a ribose and instead of thymine, RNA contains uracil. RNA has got various forms and functions; e.g. it serves as template during protein synthesis and it also constitutes the genome of RNA viruses.
  • Messenger RNA (abbr.: mRNA) is a ribonucleic acid which is a copy of a short part of the DNA and serves as template for the synthesis of a specific protein.

Glossary

  • Desoxyribonucleic acid (DNA) is a double-stranded, helical macromolecule encoding the genetic information of an organism.
  • A DNA polymerase is an enzyme catalysing the synthesis of DNA from a DNA template (e.g. during replication). In gene technology it is often used for the in vitro synthesis of DNA fragments.
  • Enzymes are catalysts in the living cells. They allow the execution of chemical transformations of the metabolism at body temperature.
  • A gene is a hereditary unit which has effects on the traits and thus on the phenotype of an organism. Part on the DNA which contains genetic information for the synthesis of a protein or functional RNA (e.g. tRNA).
  • A clone is a genetic identical copy of an organism that originates in a natural way from the division of one single cell. Examples for natural clones are colonies of bacteria and twins. Generating clones by genetic engineering is called cloning. Thereby, either DNA is recombined in vitro and multiplied in cell cultures or genetic identical cells or organisms are generated by transplantation of the cell nucleus from a body cell into an undifferentiated cell like egg cells or stem cells.
  • The life sciences involve the research, development, and marketing of products, technologies, and services on the basis of modern biotechnology.
  • Mutagenesis means the production of mutations caused by, for example, UV light or other kind of radiation or numerous chemicals.
  • There are two definitions for the term organism: a) Any biological unit which is capable of reproduction and which is autonomous, i.e. that is able to exist without foreign help (microorganisms, fungi, plants, animals including humans). b) Definition from the Gentechnikgesetz (German Genetic Engineering Law): “Any biological unit which is capable of reproducing or transferring genetic material.“ This definition also includes viruses and viroids. In consequence, any genetic engineering work involving these kinds of particles is regulated by the Genetic Engineering Law.
  • PCR or Polymerase Chain Reaction is a biomolecular method to amplify short DNA fragments in an easy way. Therefore, merely the DNA template, an enzyme named DNA polymerase which catalyses the amplification, short complementary oligonucleotides, which serve as starting point for the polymerase and the components of the DNA, which are called desoxynucleosidtriphosphates are needed. The amplification is controlled by several cycles of temperature changes.
  • Recombination is the process in which DNA is recombined. As a natural process, recombination takes place in sexual reproduction during meiosis. In vitro recombination involves the joining of DNA molecules of different origin using recombinant DNA technologies.
  • The ribosome is a cellular component composed of ribosomal RNA and protein. It is the site of protein synthesis using mRNA as a template.
  • Ribonucleic acid (abbr. RNA) is a normally single-stranded nucleic acid, which is very similar to DNA. It also consists of a sugar-phosphate backbone and a sequence of four bases. However, the sugar is a ribose and instead of thymine, RNA contains uracil. RNA has got various forms and functions; e.g. it serves as template during protein synthesis and it also constitutes the genome of RNA viruses.
  • Screening is a systematic test procedure that is used to identify certain characteristics within an array of samples or persons. In molecular biology screening is used to filter a designated clone out of a gen bank, for example.
  • Genetic sequences are successions of the bases adenine, thymine, guanine, and cytosine on the DNA (or uracil instead of thymine in the case of RNA).
  • A base triplet is a sequence of three nucleotides in DNA.
  • Molecular diagnostics deal with the analysis of the DNA or RNA of pathogens or body cells in order to detect certain diseases or dispositions for diseases. Furthermore, proofs of paternity are performed in this way. Those tests are based on molecular techniques like PCR (polymerase chain reaction), gene sequencing and hybridisation.
  • A tumour is a swelling of a tissue caused by abnormal cell growth, which can be benign or malignant. Benign tumours are local swellings, whereas malign tumours may seed off and spread into other tissues, causing secondary growths (metastases).
  • Biochemistry is the study of the chemical processes in living organisms. Therefore it touches the studies of chemistry and biology as well as physiology.
  • Molecular biology deals with the structure, biosynthesis and function of DNA and RNA and their interaction with each other and with proteins. Molecular data can lead to an improved understanding of the reasons for diseases and can help to improve the mode of action of drugs.
  • Expression means the biosynthesis of a gene product. Usually, DNA is transcribed into mRNA and subsequently translated into proteins.
  • Fluorescence is the spontanous emission of light in a certain wavelength after excitation of a molecule with light of another wavelength.
  • Messenger RNA (abbr.: mRNA) is a ribonucleic acid which is a copy of a short part of the DNA and serves as template for the synthesis of a specific protein.
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