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Biopharmaceutical biology & chemistry overview
Evolving terminology for emerging technologies

Suggestions? Comments? Questions? Mary Chitty  mchitty@healthtech.com
Last revised November 14, 2013



Q: Do you see any profound intellectual ideas taking shape in this post- genome era? (put to David Botstein (Professor and Chairman, Dept. of Genetics, Stanford Univ., US) in an interview on the Incyte Genomics website ) Dr. Botstein: Yes. In my mind, the most profound thing - in terms of the really big picture- is what I think of as the grand unification of biology. It is no longer debatable that all organisms are in one giant taxonomic group. There is no fundamental difference between prokaryotes and eukaryotes that is at the level of the difference between chemistry and physics or between a sun and a planet. Nothing like that is true. Until quite recently, many, many of my colleagues believed that difference existed. The corollary is that what you learn about one organism is likely to impact, and very possibly explain, phenomena in another organism. You see that in the literature every day now. ... That is a very big deal. http://www.incyte.com/3_0browser/dbotstein_10_00/question_05.shtml

Finding guide to terms in these glossaries Genomic biology Site map  Glossaries & taxonomies Site Map

Biology for non-biologists: Basic genetics & genomics

alternative splicing: The production of two or more distinct mRNAs from RNA transcripts having the same sequence via differences in splicing (by the choice of different exons). Mouse Genome Informatics http://www.informatics.jax.org/glossary/alternative_splicing

Recent genome- wide analyses of alternative splicing indicate that 40- 60% of human genes have alternative splice forms, suggesting that alternative splicing is one of the most significant components of the functional complexity of the human genome. Here we review these recent results from bioinformatics studies, assess their reliability and consider the impact of alternative splicing on biological functions. Although the 'big picture' of alternative splicing that is emerging from genomics is exciting, there are many challenges. High- throughput experimental verification of alternative splice forms, functional characterization, and regulation of alternative splicing are key directions for research. B. Modrek, C. Lee, "A genomic view of alternative splicing" Nature Genetics30 (1) :13- 19, Jan. 2002  Gene definitions 

apoptosis: One of the two mechanisms by which CELL DEATH occurs (the other being the pathological process of NECROSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and  appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA (DNA FRAGMENTATION) at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth. [MeSH, 1993]   If someone could figure out how to make fat cells undergo apoptosis (without harmful side effects) they could make a bundle. Related term: programmed cell death.  Cell biology glossary

biomolecules: An organic molecule, part of a living organism. Includes proteins, DNA, RNABiomolecules glossary

codon: The sequence of three consecutive nucleotides that occurs in mRNA which directs the incorporation of a specific amino acid into a protein or represents the starting or termination signals of protein synthesis. IUPAC Biotech, IUPAC Medicinal Chemistry

A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE). MeSH, 1991  Sequences, DNA & beyond glossary

combinatorial biology: Involves genetic manipulation of bacteria and fungi that produce complex natural products. This technology includes construction of large libraries of recombinant microbes capable of generating novel organic molecules and engineering secondary metabolite biosynthetic pathways to modify valuable biologically active microbial metabolites. ASB [Am Soc. Biomechanics] Newsletter, June 1998   http://asb-biomech.org/newsletter/V11N1/guest.html  Biomaterials & bioengineering glossary

expression: The cellular production of the protein encoded by a particular gene.  The process includes transcription of DNA, processing of the resulting mRNA product and its translation into an active protein.  N.B. A recombinant gene inserted into a host cell by means of a vector is said to be expressed if the synthesis of the encoded polypeptide can be demonstrated.  IUPAC Bioinorganic, IUPAC Compendium

A description as to how a gene demonstrates a phenotype.  This can range from production of a mRNA to a disease.  If a disease gene carrier shows signs of the disease gene, then that gene is expressed.  Note that an individual must carry the disease gene and be penetrant  for it before the term expression is utilized. [NHLBI]  Narrower terms gene expression, protein expression. Expression glossary  

Gene OntologyTM (GO): The goal of the Gene OntologyTM Consortium is to produce a dynamic controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. http://www.geneontology.org/   Functional genomics glossary

genes, human:  At the 2000 Cold Spring Harbor Genome conference [May 10-14] "one of the hotly debated topics was the number of human genes. This has been estimated at anything from 35,000 to 150,000. Considering the spread of opinion, the only way to resolve was to get people to bet on it … This led to an interesting debate on the definition of a gene … and how to assess that number. A gene is a set of connected transcripts. A transcript is a set of exons via transcription followed (optionally) by pre- mRNA splicing. Two transcripts are connected if they share at least part of one exon in the genomic coordinates. At least one transcript must be expressed outside of the nucleus and one transcript must encode a protein. "Genesweep" Ensembl, European Bioinformatics Institute, UK http://www.ensembl.org/Genesweep/  With the publication of the Human Genome Project draft sequence in Feb. 2001 we learned that the number of genes (about 30,000) seems to be many fewer than expected, but the number of proteins per gene, with alternative splicing (two to three, instead of one) is greater.  More surprises seem sure to be in store.  Gene Definitions  

gene nomenclature, human: There is "currently no official nomenclature for human genes, however, the Human Gene Nomenclature Committee (part of HUGO) is currently trying to establish a nomenclature standard and does have a recommended format. The Human Gene Nomenclature Committee is the accepted authority for establishing these standards." dbSNP FAQ, NCBI, US http://www.ncbi.nlm.nih.gov/SNP/get_html.gene nocgi?whichHtml=faq      Nomenclature, genes & beyond

genetic maps: The value of the genetic map is that an inherited disease can be located on the map by  following the inheritance of a DNA marker present in affected individuals (but absent in unaffected individuals), even though the molecular basis of the disease may not yet be understood nor the responsible gene identified. Genetic maps have been used to find the exact chromosomal location of several important disease genes, including cystic fibrosis, sickle cell disease, Tay- Sachs disease, fragile X syndrome, and myotonic dystrophy.  [Primer on Molecular Genetics, Oak Ridge National Lab, US]

Can be cytogenetic, linkage, or physical maps. Starting genetic maps is easier than finishing them.   Maps- genomic & genetic glossary  

genomic DNA gDNA: The entire length of DNA, including non coding regions. (Sometimes called gDNA.) CHI Bioinformatics report  DNA which includes exons and introns, coding and noncoding regions. Compare with cDNA DNA Glossary

glycomics: Glycans are complex, making it hard to exploit their therapeutic possibilities. However, promising new tools and methodologies are available to tackle the most pressing questions, such as: How to purify the glycoproteins? How to analyze the “sticky” substance?  What is necessary to get more information on the compound, its structure and binding specificities? After deciding on a target compound - what are the next steps? What are the weaknesses and strengths of analytical tools used? How can you compare various methods? And finally, how do you turn your investment in glycoproteins and carbohydrates into a success story   Glycosciences glossary

housekeeping genes: In theory, expressed in all genes. Contrast with luxury genes. Genes that encode housekeeping proteins. Specific housekeeping genes can be used to normalize gene expression data. Not usually the gene of greatest interest for functional studies. Gene categories glossary

hypothetical protein: Many of the gene products of completely sequenced organisms are "hypothetical" –  they cannot be related to any previously characterized proteins – and so are of completely unknown function. ... As each [completely sequenced] organism’s genome is analyzed about one third of the observed open reading frames (ORFs), although conserved among several organisms, encode for "hypothetical‘ proteins. E Eisenstein et al "Biological function made crystal clear – annotation of hypothetical proteins via structural genomics" Current Opinion in Biotechnology 11(1): 25-30 Feb. 2000  Protein categories glossary 

luxury genes: Specialized genes with specific functions. Compare with housekeeping genes. Gene categories 

model organisms: Model organisms are of key importance in both creating databases of gene sequences for homology searching, and as platforms for investigating the biology of genes of interest. Over the last few years, the use - and sophistication - of such models has increased substantially. Findings from the recent publications by the Human Genome Project and Celera Genomics support that homology between human and animal- model genes and proteins is significant, particularly among vertebrate species. Still, the conservation of genes and genetic pathways between humans and invertebrate organisms is great enough that some of these organisms have become critical model systems. Related terms: knockdown, knockin, knockout   Model & other organisms glossary  

modular biology: Leland H. Hartwell, et. al. From Molecular to Modular Cell Biology, Nature 402 (suppl)., C47-C52, 1999 http://sysbio.harvard.edu/csb/research/pdfs/Murray_ModularBiology.pdf 

pharmacophore: The ensemble of steric and electronic features that is necessary to ensure the optimal supramolecular interactions with a specific biological target structure and to trigger (or to block) its biological response. Does not represent a real molecule or a real association of functional groups, but a purely abstract concept that accounts for the common molecular interaction capacities of a group of compounds towards their target structure. Can be considered as the largest common denominator shared by a set of active molecules.  IUPAC Medicinal Chemistry Drug targets glossary

post-translational modifications: Proteins once synthesized on the ribosomes, are subject to a multitude of modification steps. They are cleaved (thus eliminating signal sequences, transit or pro- peptides and initiator methionines); many simple chemical groups can be attached to them … as well as some more complex molecules, such as sugars and lipes. Finally they can be internally or externally cross- linked. More than a hundred different types of post- translational modifications are currently known (Aug. 1999) and many more are yet to be discovered. The complexity due to all these modifications is compounded by the high level of diversity that alternative splicing can produce at the level of sequence. Thus the number of different protein molecules expressed by the human genome is probably closer to a million than to the hundred thousand generally considered by genome scientists. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 Amos Bairoch* Rolf Apweiler  Nucleic Acids Research 28 (1): 45-48  http://nar.oxfordjournals.org/content/28/1/45.full?ref=klasshop.com      Proteins glossary

protein structure: Given that proteins carry out their functions as three- dimensional structures (e.g., that determine the active sites of enzymes and the ligand- binding sites of receptors), a greater ability to work with three- dimensional structures and to look for similarities in these structures (between the products of different genes) is expected to yield improved functional information. CHI Functional Genomics report Protein structure glossary   

RNAi RNA interference:  RNA interference (RNAi) has been a continually evolving area of research. Discovered primarily as a technique for gene silencing, RNAi has now emerged as a screening tool for target identification and validation in early drug discovery. Since establishing its presence as a screening tool, RNAi is now looking to make an impact in the therapeutic arena. Several RNAi-based compounds are already in various stages of clinical testing. Although still in its infancy, RNAi therapeutics are making rapid progress in the clinic, learning from mistakes made in the past by other gene therapy approaches.    RNA glossary 

SNP Single Nucleotide Polymorphism: A point mutation that occurs in greater than 1% of the population. May serve as hereditary markers if they are either within a gene or regulatory region or associated with a gene. Occur every 100-300 bases. Narrower terms: SNPs anonymous SNPs, cSNPs, candidate SNP, pSNP, rSNP, synonymous SNP. Related terms idiomorphism SNPs & other genetic variations glossary

stem cells:  Commercialization of stem cells can potentially help to treat an astounding variety of medical conditions. After a slow start, the stem cell age is finally poised to begin, as numerous factors converge to catapult stem cell technology into the medical mainstream. This report considers: the current state of stem cell science and technology  Supplies and services, Major applications of stem cell science, Sources of funding, regulatory hurdles, and the commercial outlook, IP challenges, public perception, bioethical concerns, and diversity in policies. Stem cell science is on the precipice of becoming big business. These enigmatic cells lie at the heart of a fledgling technology with great clinical promise. Insight Pharma Reports, Stem cells come of age, 2008  Stem cell glossary

systems biology:  researchers at ISB seek to understand not only each constituent of a biological network but also how all of a network’s constituents function together. They use cutting-edge technologies to gather as much information as they can about a biological system. They then use this information to build mathematical and graphical models that account for the behavior of the system. They test these models by gathering additional data, often by perturbing a system through genetic or environmental changes. In this way, they build an understanding of biological systems that can be used, for example, to explore what goes wrong when a biological system becomes diseased and how to treat or prevent that disease. ISB Institute for Systems biology http://www.systemsbiology.org/about-systems-biology. Bioinformatics glossary

Bibliography

Alpha glossary index

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.

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