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'. Bio 2900 Computer Applications in Biology Bioinformatics Presented by Frank H. Osborne, Ph. D. Bioinformatics • Bioinfonnatics is the computational branCh of molecular biology. • It involves using computen in the analysis of DNA, RNA and protein sequences. • It is part ofa larger field of biology called Computational Biology. 02005 Protein Synthesis • Generally, we begin with DNA. • DNA is transcribed to produce RNA. • RNA is then translated to produce protein. • The protein is the result of the expression ofa gene. Amino Acid Table Amino Acids • Proteins are made of amino acids. There are abOut 20 that are generally used in protein molecules. • A set of three-letter abbreviations is used for the amino acids in biochemistry. • The International Union of Pure and Applied Chemistry (lUPAC) has created one-letter abbreviations to ease work in bioinformatics. Additional Amino Acid Codes • Additionally, IUPAC recognizes other code letten for special situations. • There are an additional four codes that maybe used. 1 'Additional Amino Acid Code Table DNA • Deoxyribonucleic acid (DNA) is made up of purine bases (adenine and guanine) and pyrimidine bases (cytosine and thymine). Bases are part of nucleotides which are formed using the sugar deoxyribose. Nucleotides are connected by condensation reaction from the 5'08 to the 3'08. RNA DNA • For DNA sequences, the IUPAC has established the one-letter codes shown below. Gene structure • A gene is a sequence of bases of DNA. It begins at a location known as a promoter and ends at another location called the terminator. _ .... • The IUPAC one-letter codes for RNA are shown below. Gene expression • Genes are expressed by transcription and translation of DNA., DNA is first transcribed to make messenger RNA. The genetic code of the messenger RNA is translated into protein. T........... 2 Transcription RNA polymerase o o Transcription uses DNA-dependent RNA o initiation, elongation and termination. Note consists of a core enzyme of four polypeptides and another factor called a factor. Core enzyme = that these are not the same as initiation, elongation and termination of protein synthesis, which make up the process of translation. - 2 a. identical subunits - p, p' similar but different proteins o o Transcription consists of three stages called polymerase. RNA polymerase holoenzyme Holoenzyme = core enzyme + a factor There are different types of promoten that are recognized by different a facton. Stages of transcription o Initiation Translation o - RNA polymerase attaches to the promoter. An open compies. forms. o Elongation. The mRNA molecule is translated into protein using the standard genetic code. There are some exceptions, especially during protein synthesis in mitochondria. - RNA polymerase moves along the DNA molecule making a molecule of RNA as It travels. o Termination - RNA polymerase reaches the terminator. The RNA is released. Stages of translation o Initiation Gene organization in Bacteria o - Ribosomes bind to the ribosome-binding site on the mRNA molecule known as the Sbine Dalgarno sequence adjacent to AUG. o Elongation - Transfer RNA brings each amino acid to the amino-acyl site according to tbe specified codons. o Termination - The completed protein is released from tbe peptidyl site. o A cisITon is a distinct region of DNA that codes for a particular polypeptide. The term is used in the context of a protein which is made up of several subunits, each of which is coded by a different gene. An operon is a common form of gene organization in bacteria. _ T_ IMI • II • II • II 4 11M DNA ~- • • • • 0(!)G)@ ... 3 Genotypes and phenotypes Regulation of gene expression • The genotype is an actual gene in the chromosome. The phenotype is the observed effect of that gene. • Genotypes are given using italic letten. Phenotypes are written in ordinary, regular letten. Thus, two of the tryptophan genes in E. coli would be tTpA and trpB. When expressed, they produce polypeptides. The tTpA gene prodoces trpA (TrpA) polypeptide and the tTpB gene produces trpB (TrpB) polypeptide. The lac operon • The lac operon contains the genes necesary to utilize lactose. Lactose is a ~galactoside sugar containing galactose ~(1,4) as shown below. CH2 0H CHZOH ~~H H~,,~ ~ OH OH Regulation of gene expression Regulation of gene expression Products of the lac operon • The lac operon codes for three proteins; LacZ, LacY, LacA; which are directly involved in galactoside (lactose) utilization. Function of the lac operon • lacJ - gene for the lac repressor protein • lacPI· promoter for fucl • lacP - promoter for lac operon • lacO - operator: binding site for the repressor Lad is a repressor that binds to the promoter (lacp) and prevents the gene from being transcribed. This type of control is known as transcriptional regulation. - LacZ - b-D-galac:tosldue (EC 3.1.1.13) - LacY· galactoside permease (M protein) - LacA - galactoside autyltransferase (EC 2.3.1.18) • These enzymes appear adjacent to each other on the E. colt chromosome. They are preceded by a region of the cbromosome responsible for tbe regulation of these genes. Induction and repression Structure of the lac operon • When lactose is present it induces the operon by binding to the repressor and changing its shape, causing it to faU off the operator. • When lactose is removed, the repressor goes back to its original sbape and can bind to the operator again. • Because the repressor binds to the operator, the RNA polymerase is said to be primed, meaning that it is ready to use as soon as the block comes off the operator. 4 Gene Expression in Eukaryotes Gene Expression in Eukaryotes • DNA in eukaryotic organisms is organized into chromosomes. The eukaryotic chromosome consists of DNA interwound with proteins known as histones. • Much eukaryotic DNA has either no function or unknown function. Unlike bacteria, only about 10% of eukaryotic .DNA codes for proteins. • Euksryotic DNA has numerous repeated nucleotide sequences. The protein-coding regions are separated by nonoCoding regions. • The non-coding regions are called introns• • The coding sequences that are expressed as protein are called exons• Transcription in Eukaryotic Cells The End I I ! I 5