Bioinformatics lecture 1

Editor's Notes

• #4: An appreciation ___ large amount of information about Living things. Applications of BI to _____molecular biology, medicine, pharmacology, biotechnology, agriculture, forensic science, anthropology etc. A useful knowledge of the techniques by which, through the WWW, we access the data and the methods for their analysis.
• #5: A sense of optimism that the data and methods of bioinformatics will create profound advances in our understanding of life, and improvements in the health of humans and other living things.
• #6: Molecular biology -Genetics & Protein Biochemistry
• #10: Computational biology  involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. [1]  
• #13: Genomics existed before any genomes were completely sequenced, but in a very primitive state
• #15: Related Fields: Pharmacogenomics The application of genomic methods to identify drug targets For example, searching entire genomes for potential drug receptors, or by studying gene expression patterns in tumors i nvestigation of genetics and drug response: the study of the relationship between a specific person's genetic makeup and his or her response to drug treatment ( takes a singular verb ) Microsoft® Encarta® 2007. © 1993-2006 Microsoft Corporation. All rights reserved.
• #18: theories of Heredity Developed his theories through the study of pea pods. Studied them “for the fun of the thing”
• #20: This concept was later fully developed into the concept of chromosomes
• #23: Studied plant and animal germ cells distinguished between body cells and germ cells and proposed the theory of the continuity of germ plasm from generation to generation (1885) Developed the concept of meiosis
• #27: British microbiologist In 1928, Studied the effects of bacteria on mice Determined that some kind of “transforming factor” existed in the heredity of cells Frederick Griffith (1881-1941), British microbiologist who discovered a phenomenon called transformation—meaning an alteration of hereditary characteristics—in the Streptococcus pneumoniae bacterium. Griffith’s work paved the way for later experiments, which proved that deoxyribonucleic acid (DNA) is the material within cells that passes on genetic traits. He is considered by some to be the father of molecular biology. Avery's team purified this substance and found it was pure DNA. Avery published the results of his research in 1944. Transformation is the process by which bacteria take up unpackaged DNA from the environment. Only cells that are “competent” can receive DNA in this fashion. Cells can be made competent, however, via a routine procedure in molecular labs where introduction of foreign DNA into bacteria is fundamental to recombinant DNA technology. In transduction, viruses move DNA from one cell to another.
• #29: Martha Chase: she participated in the famous “blender experiment,” also known as the Hershey-Chase experiment. This experiment, which earned Alfred Day Hershey a Nobel Prize, used a kitchen blender to separate the protein coats of simple viruses called bacteriophages from their DNA cores. Hershey and Chase showed that the isolated DNA was infectious, but that without the DNA, the protein coats were not. Microsoft ® Encarta ® 2007. © 1993-2006 Microsoft Corporation. All rights reserved.
• #37: 1980: submission of the whole genome sequence of adenovirus to GenBank(R), the National Institutes of Health genetic sequence database. The submission marks the first time that a new method has been used to sequence a whole genome since Walter Gilbert and Frederick Sanger won the Nobel Prize in 1980 for the invention of DNA sequencing in 1977. The whole genome sequence (GenBank accession nos. AY370909, AY370910, and AY370911) was generated in less than one day using the first technology ever designed to sequence whole genomes, not one gene at a time. More importantly, this was accomplished by using a new platform that is scaleable to larger genomes. The bacteriophages Rt7 and Qβ have RNA as their genetic material. The single stranded RNA contains only three genes, One codes for A protein the second for coat protein, and the third for one of four subunits of replicase. (The other three units of replicase are host proteins). Polyoma or SV40 viruses have 5-10 genes and their chromosomes are only 1.7 microns in length. The single stranded DNA virus ØX174 has DNA which codes for 9 Proteins. The bacterial virus lambda has about 40 genes and T4 has over a hundred genes. The number of genes in viruses ranges from only three in the simplest viruses to about 250 in the most complex ones.
• #38: Although there is some relationship between the number of genes and the complexity of an organism there in no strict correlation between apparent genetic complexity and the DNA content per haploid nucleus. Thus some fishes and amphibians contain 10 to 20 times more DNA than humans. Moreover, the size of the genome varies over a 20-fold range within the species of a phylum kilo base pairs = 1000 bp; Mb =  mega base pairs  = 1000000 bp; 1 million bp GBP: 1000 million bp
• #39: Comparative Genomics: the management and analysis of the millions of data points that result from Genomics__ Sorting out the mess Functional Genomics: identifying gene functions and associations Strucutural Genomics: future plans of structural genomics efforts around the world and describes the possible benefits of this research
• #42: Recall the concept of differentiation from embryology.
• #44: The haploid human genome contains ca. 23,000 protein-coding genes , far fewer than had been expected before its sequencing. [1][2]  In fact, only about 1.5% of the genome codes for  proteins , while the rest consists of  non-coding RNA  genes, regulatory sequences ,  introns , and  noncoding DNA  (once known as "junk DNA"). [3] Surprisingly, the number of human genes seems to be less than a factor of two greater than that of many much simpler organisms, such as the  roundworm  and the  fruit fly . However, human cells make extensive use of  alternative splicing  to produce several different proteins from a single gene, and the human  proteome  is thought to be much larger than those of the aforementioned organisms.[ citation needed ] Besides, most human genes have multiple  exons , and human  introns  are frequently much longer than the flanking exons.[ citation needed ]
• #47: Prions epigenetics  is the study of  heritable  changes in  phenotype  (appearance) or  gene expression  caused by mechanisms other than changes in the underlying  DNA  sequence, hence the name  epi-  (Greek:  επί - over, above)  - genetics . These changes may remain through  cell   divisions  for the remainder of the cell's life and may also last for multiple generations. However, there is no change in the underlying  DNA  sequence of the organism; [1]  instead, non-genetic factors cause the organism's genes to behave (or "express themselves") differently. [2] One example of epigenetic changes in  eukaryotic  biology is the process of  cellular differentiation . During  morphogenesis , totipotent   stem cells  become the various  pluripotent   cell lines  of the  embryo  which in turn become fully differentiated cells. In other words, a single fertilized egg cell – the  zygote  – changes into the many cell types including neurons, muscle cells, epithelium, blood vessels etc. as it continues to  divide . It does so by activating some genes while inhibiting others
• #48: The normal role of Prions is not known. It probably protects cells from injury. All known mammalian prion diseases are caused by the so-called prion protein,  PrP . The endogenous, properly-folded, form is denoted PrPC (for  c ommon  or  c ellular ) while the disease-linked, misfolded form is denoted PrPSc (for  Sc rapie , after one of the diseases first linked to prions and neurodegeneration.) [9][10]  The precise structure of the prion is not known, though they can be formed by combining PrPC, polyadenylic acid, and lipids in a  Protein Misfolding Cyclic Amplification  (PMCA) reaction. [11] Proteins showing prion-type behavior are also found in some  fungi , which has been useful in helping to understand mammalian prions. Interestingly,  fungal prions  do not appear to cause disease in their hosts and may even confer an evolutionary  advantage through a form of protein-based  inheritance . [12]