Review 2 The structure of DNA Structurally it is a pentose 2 carbon is deoxy Base hangs off of the 1 carbon Purines A and G is a 6 membered and 5 membered ring Pyrimidines T C is a 6 membered ring Hydrogen bonds hold together the base pairs Triphosphate hangs off of the 5 carbon Nucleotides are the building blocks for DNA Phosphodiester bonds hold together two nucleotides To make a chain of nucleotides we polymerize them by a dehydration synthesis The phosphate hanging off of the 5 carbon connects to the 3 carbon DNA replication Semi conservative replication replicated DNA is made up of one new strand an one old strand Meselson Stahl experiment Old DNA contains N 15 isotope and the new DNA contains N 14 isotope Time zero one DNA molecule where both strands are N 15 Time one two DNA molecules where both have one strand of N 15 and one strand of N 14 Time two four DNA molecules where two have one strand of N 15 and one strand of N 14 and two have both strands of N 14 DNA polymerase promotes the assembly of nucleotides Primer a piece of DNA that matches the template that can use the OH at the 3 carbon end to grab the next nucleotide to extend the strand Primase the enzyme that makes primer New strand is created in the 5 to 3 direction therefore it copies from the template strand in the 3 to 5 direction There is continuous replication of one strand and discontinuous replication of the other strand Ligase joins the okazaki fragments together Topoisomerase the two DNA strands are separated cut moved around the other strand and reattached Proof reading Exonuclease activity that moves in the 3 to 5 direction removing bases Endonuclease Mismatch detection which detects cuts and tries again It knows the old strand because of the methyl on the old strand Translation One strand of RNA is mRNA and the other is tRNA The ribosome is the protein factory that scans the codons Every three bases of mRNA encodes for some amino acid Start codon AUG which encodes for methionine MET Stop codon UAA UAG UGA Bacterial viruses bacterialphage Viruses cause bacterias to burst open letting lots of bacterialphage burst out Capsid the protein cell of a virus Replication Central dogma DNA RNA Protein Eukaryotes there are origins of replication Telomerase At the end of the strand called telomers we add the sequence TTAGG Prokaryotes they have circular DNA which makes replication easier Viruses there can be linear or circular double stranded DNA there can also be single stranded DNA or even RNA dsDNA virus hijacks the host s machinery ddDNA virus hijacks the host s machinery dsDNA virus needs RNA dependent RNA polymerase ssRNA which is the same as mRNA encodes the very code to make its own polymerase Uses RNA directed RNA polymerase ssRNA which is the same as tRNA brings along its own polymerase Uses RNA directed DNA polymerase Reverse transcriptase RNA makes DNA which can then be copied into another strand of DNA producing double stranded DNA Viruses insert DNA into the host chromosome and that gene is then transcribed and can be replicated Retroviruses viruses that replicate in a host cell through the process of reverse transcription Transcription Prokaryotes the gene is transcribed to make mRNA Eukaryotes the gene is transcribed to make mRNA 5 cap the 5 carbon modi cation put on the mRNA PolyA tails the long tail of A s put on the 3 carbon Splicing DNA produces immature mRNA which is then spliced into make RNA Introns the thrown out bits Exons the kept in bits Alternative splicing The original transcript can be spliced in alternative ways producing different mature RNA and proteins Beta galactosidease and Beta globin Beta gal found in E coli encodes an enzyme in the metabolism of sugar E coli graves sugar because it uses glucose to make ATP through glycolysis If there is no glucose lactose can be used Lactose is a disaccharide made up of galactose and glucose Beta galactosidease breaks apart the simple sugars in lactose If glucose is present lactose will not be broken down Lac operon involved in the breakdown of lactose the promoter starts the transcription which is encoded into three proteins from lac Z lac Y and lac A regions Lac Z encodes beta gal Lax Y encodes lactose permease The lac repressor protein can form a physical association with lactose or the lac operon If lactose is not present the repressor binds to the operon If lactose is present the repressor binds to lactose changing the shape of the repressor so RNA polymerase can bind to the promoter When lactose and glucose are not present there are high levels of cAMP a product of glycolysis The lac repressor protein binds cAMP which sits down and make the RNA polymerase stabilize cAMP is an activator protein it increases transcription when glucose levels are low Beta globin found in homo sapiens encodes one of the subunits of hemoglobin which is an oxygen transporter Hormone receptors in mammals Estrogen binds to the estrogen receptor which is bound to something holding it in the cytoplasm When estrogen and the estrogen receptor move to the nucleus and sits down at the estrogen responsive element helping transcription to occur Beta globin Hemoglobin sits on chromosome 11 and has alpha and beta subunits There are exactly three exons and the start and stop codons are within exons 1 and 3 respectively The non translated regions are known as the 5 and 3 non translated region Mutations Missense one nucleotide is affected a point mutation Conservative missense the change in the amino acid is not problematic Non conservative missense dramatic change that affects the entire protein Deletion Insertion causes a frame shift Least problematic at the end Nonsense changes a codon to a stop codon The protein is shortened Silent change a nucleotide in the sequence but it encodes for the same amino acid Promoter causes the loss of a promoter The transcript is not made Splicing splicing signals can be changes the RNA will not be recognized and spliced Poly A site the sequence would not get cut and would not get its poly A tail it would be degraded because the polyA tail protects the message History of cancer Avian leukemia virus with SRC produces RSV SRC causes growth SRC codes for a protein called kinase which is a tyrosine kinase Kinases add phosphates Cancer results when cells grows and divides without end Neoplasm a tumor of cells continuing to divide Benign when the neoplasm stays in one place Malignant when the neoplasms invades the surrounding tissue Metastasis
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