Lecture 19A. DNA computing What exactly is DNA (deoxyribonucleic acid)? DNA is the material that contains codes for the many physical characteristics of every living creature. Your cells use different codes to determine what functions to carry out, just as you use code to communicate. The cell nuclei of all eukaryotic organisms contain DNA and each cell contains all the genetic code needed to assemble the entire organism. The amount of information involved requires the individual DNA strands to be extremely long. Each cell contains about 3 cm of DNA. The fact that this long molecule fits into a cell of around a few microns across is because DNA is very thin (2 nm in diameter). The building blocks DNA gets its name from deoxyribonucleic acid which is a type of nucleic acid. Nucleic acids are made up of polynucleotide chains which are formed by many nucleotides bonded together. Phosphate, Ribose sugar, and BasesDNA and RNA There are two different kinds of sugars in a nucleotide, deoxyribose and ribose. If the polynucleotide chain forms DNA then the sugars in its nucleotides are deoxyribose while nucleotides containing ribose as its sugar form RNA. The Bases There are five different bases in a nucleotide. These bases are adenine, cytosine, guanine, thymine, and uracil. Uracil is only found in RNA, while thymine is only found in DNA. Each base is identified by the first letter in its name. DNARNAAdenine (A) Adenine (A) Cytosine (C) Cytosine (C) Guanine (G) Guanine (G) Thymine (T) Uracil (U)Polynucleotide chain Nucleotides bond together in a chain to form polynucleotide chains such as the one below. In a polynucleotide chain, there are open ends. The open phosphate end is called the 5' end while the open sugar end is called the 3' end. A section of a polynucleotide chain with each individual nucleotide bonded together.The Base Pairing Chargaff's Rule: A=T, G=C. By using Chargaff's rule Watson and Crick discovered that Thymine paired with Adenine and Guanine with Cytosine. They also discovered that a hydrogen bond was obtained when the bases were paired together in this way. A-T G-C In a DNA strand Adenine is always paired with Thymine, and Guanine is always paired with Cytosine.Double helical DNA A DNA strand consists of two polynucleotide chains bonded together by their nitrogenous bases, thus one looks like this.Proteins Proteins are sometimes called Polypeptides, since they contain many Peptide Bonds The peptide bond is an amide bond R is one of the 20 amino acidsAmino Acids Grouped Alphabetically Letter Amino Acid Name Abrev. Structure LetterAmino Acid Name Abrev. StructureA Alanine Ala M Methionine Met C Cysteine Cys N Asparagine Apn D Aspartic Acid Asp P Proline Pro E Glutamic Acid Glu Q Glutamine Gln F Phenylalanine Phe R Arginine Arg G Glycine Gly S Serine Ser H Histidine His T Threonine Thr I Isoleucine Ile V Valine ValK Lysine Lys W Tryptophan Trp L Leucine Leu Y Tyrosine Tyr Grouped by Characteristics Transcription (reading) DNA contains the blue print for the chemicals that make up our body. DNA tells the body what proteins to make and the proteins carry out the functions. How does it work? Proteins are made of Amino Acids which are bonded together in chains during transcription. The genetic code The genetic code consists of 64 triplets of nucleotides. These triplets are called codons. With three exceptions, each codon encodes one of the 20 amino acids used in the synthesis of proteins. That produces some redundancy in the code: most of the amino acids being encoded by more than one codon. One codon, CAT serves two related functions: • it signals the start of translation • it codes for the incorporation of the amino acid histidine (Met) into the growing polypeptide chain . TTT Phe TCT Ser TAT Tyr TGT Cys TTC Phe TCC Ser TAC Tyr TGC Cys TTA Leu TCA Ser TAA STOP TGA STOP TTG Leu TCG Ser TAG STOP TGG Trp CTT Leu CCT Pro CAT His CGT Arg CTC Leu CCC Pro CAC His CGC Arg CTA Leu CCA Pro CAA Gln CGA Arg CTG Leu CCG Pro CAG Gln CGG Arg ATT Ile ACT Thr AAT Asn AGT Ser ATC Ile ACC Thr AAC Asn AGC Ser ATA Ile ACA Thr AAA Lys AGA ArgATG Met* ACG Thr AAG Lys AGG Arg GTT Val GCT Ala GAT Asp GGT Gly GTC Val GCC Ala GAC Asp GGC Gly GTA Val GCA Ala GAA Glu GGA Gly GTG Val GCG Ala GAG Glu GGG Gly The genetic code is almost universal. The same codons are assigned to the same amino acids and to the same START and STOP signals in the vast majority of genes in animals, plants, and microorganisms. However, some exceptions have been found. DNA to RNA Remember the structure of DNA and chromosomes. There are multiple genes on each DNA strand that spans the chromosome. When the time comes to make a certain protein from the code of a certain gene, the cell does not need to read the whole DNA strand. Instead, it only reads that gene, this being the most sensible thing to do. There are a few enzymes that help this process to work. The first of which are the Basal Factors which are a set of proteins that mark the promoter region or the beginning of the gene that is to be read. The end of the gene is marked by the Enhancer Region with the Activator proteins (transcription factors). From the promoter region and the enhancer region, transcription will take place. The first step begins with the Bending protein traveling along the gene to a spot between the enhancer region and the promoter region. Once at this halfway spot the protein bends the DNA strand so that the activator proteins at the enhancer region are toughing the basal factors at the promoter region. This combining of the proteins stimulates RNA polymerase to do its work. RNA polymerase is an enzyme that more or less does the same thing that DNA helicase and polymerase do. It begins at the promoter region of the gene and unzips the DNA strand. Next, it constructs a polynucleotide chain of RNA (ribonucleic acid) that compliments the DNA bases. This enzyme pairs RNA nucleotides with the original DNA nucleotides with the rule of C=G and A=U. U being Uracil takes the place of Thymine on the RNA strand that is forming. As separate RNA nucleotides pair up with the bases of the DNA strand the enzyme bonds them into a polynucleotide chain of messenger RNA (mRNA). When the RNA polymerase is finished, it drags the mRNA strand away from the DNA strand outside of the