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 Bases
DNA 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. DNA Adenine (A) Cytosine (C) Guanine (G) Thymine (T) RNA Adenine (A) Cytosine (C) Guanine (G) 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 acids
Letter Amino Acid Name Amino Acids Grouped Alphabetically Abrev. Structure Letter Amino Acid Name Abrev. Structure A 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 Val
K Lysine Lys W Tryptophan Trp L Leucine Leu Y Tyrosine Tyr Transcription (reading) Grouped by Characteristics 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 Arg
ATG 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 nucleus of the cell into the cytoplasm while the DNA strand "zips" up to its original form. Introns Scientists have determined that up to 70 percent of the RNA that is made through transcription by copying DNA is unneeded. One term for this unneeded DNA is "Junk DNA". It is not known why there is so much junk DNA, but it possibly could lower the chances of mutations in the DNA sequence that could cause a disease, or a deformity. This could be true since the mutations have a greater chance of happening to the junk DNA since there is more of it. Since there is so much "Junk DNA" in the mrna strand, it needs to be removed so the correct protein can be assembled. As the mrna is taken into the cytoplasm of the cell, an enzyme called a splice some runs along the polynucleotide chain to determine what part of the DNA strand
should be cut out and discarded. A string of unnecessary mrna is called an intron. When the slice some finds an intron it pulls the RNA together so that the intron loops away from the strand. Then it cuts out the intron and bonds the two ends together. Once the introns are cut out of the mrna it is taken into the cytoplasm to undergo the last stage of transcription, protein synthesis. Protein Synthesis Once the mrna is outside of the nucleus, the protein is made. A special component of the cell called a Ribosome runs along the strand to determine which amino acids to bond together to make a protein. The ribosome reads every base in groups of three (codons). There is a different kind of RNA called trna or transfer RNA. Transfer RNA units are simple because they are made of RNA which is attached to a certain amino acid. On these units of trna a special group of three bases distinguish what amino acid is attached to it. This special group of three bases is called an anti-codon because the ribosome pairs up anti-codons with codons. Each anti-codon is the exact compliment of bases as its codon. For example: Codons GAC UCC CGG UAU Anti-codons CUG AGG GCC AUA Transformation of genetic code from DNA to the ribosome for protein synthesis via messenger RNA.
Ribosome Back to the ribosome. As the ribosome runs along the mrna strand, it reads the codons. When the ribosome comes to the codon, AUG, it places its matching anti-codon next to it and uses the amino acid, methionine, that accompanies this anti-codon as the first amino acid in the amino acid chain. Then it reads the next codon and the procedure is repeated, but it now bonds the first amino acid to the second one. This process of reading the codons, matching them with their anticodons, and bonding the amino acids together is continued until the ribosome reads a triplet of UAA, UAC, or UGA. These codons tell the ribosome to stop bonding the amino acids together. Once the Ribosome is finished bonding the amino acids together into what is called a polypeptide chain (not to be confused with polynucleotide chain), named because of the type of bond between the amino acids, the protein is finished being made and transcription is complete. AUG is the start codon which tells the ribosome to begin making the polypeptide chain. UAA, UAC, and UGA are stop codons which tell the ribosome to stop making the polypeptide chain. Replication (copying) During mitosis (cell division) cells make copies of their chromosomes. The chromosomes duplicate themselves so that the cells that come from the original cell will have the same DNA. In order for this copy to be made, DNA must go through replication. Replication is the name given for the act of copying DNA strands. To begin replication, an enzyme called DNA helicase unwinds the long DNA strand. As the strand unwinds, another enzyme, DNA polymerase, travels up from the 3' end attaching complimenting bases to the unzipped strand. Then it travels down toward the 5' end connecting complimenting bases to this side of the double helix. Another DNA polymerase continues this process by traveling up the 3' end, reaching the DNA helicase (which is still "unzipping" the the DNA strand), and then traveling down the 5' end. Eventually, this process results in two strands of DNA; the cell is ready to divide.
PCR (Polymerase chain reaction)