DNA and the Gene Synthesis Repair 01 22 2014 Hershey chase experiment DNA has phosphorus but not sulfur Proteins have sulfur not phosphorous bacteria after the viruses attacked o DNA was the genetic material DNA directional 5 phosphate 3 hydroxyl o Use radioactive of each and watch to see which enters a Meselson Stahl Experiment Found that the semiconservative model for DNA is the one that is true One new and one old strand exist in replicated DNA DNA synthesis bidirectional goes both ways at same time Helicase breaks hydrogen bonds between bases unzips DNA Single stranded binding proteins keep two strands from coming back together after bonds are broken Topoisomerase relieves tension in backbone cuts the DNA allows it to unwind and then rejoins it ahead of replication fork Primase creates primer during unzipping unwinding Primer short strand of bases that has a free OH group that can combine with a DNA base to form phosphodiester bond Lagging strand discontinuous but still 5 to 3 o Okazaki fragments are short DNAs made by DNA poly o DNA polymerase removes primer RNA and puts on DNA o DNA ligase closes gaps between backbone by forming phosphodiester bonds Replicating the end of linear chromosomes Telomere end part of a chromosome no genes but repeated Lagging strand struggles to finish the entire chromosome sequences shortening the ending Telomerase extends unreplicated end has its own RNA template but creates DNA out of it most somatic cells don t have telomerase activity Fixing DNA synthesis errors DNA polymerase can proofread its errors and fix them Mismatch repair corrections are made to incorrect base pairs DNA repair can occur from radiation and other factors o Nucleotide excision repair fixes thymine dimers and other types of damage Transcription RNA processing Translation 01 22 2014 Transcription RNA polymerase synthesizes mRNA Reads the template strand to create the mRNA The non template or coding strand matches the mRNA except for having T instead of U no primer is needed for RNA polymerases 3 phases o initiation Protein subunit sigma and RNA polymerase form an enzyme together but it only binds to specific sections of DNA called promoters TATA box RNA polymerase begins synthesizing 5 to 3 RNA polymerase opens double stranded DNA and starts o Elongation making mRNA o Termination Its over when RNA polymerase transcribes a DNA sequence that makes a stop signal RNA Processing Bacteria mRNA are mature right after transcription Eukaryotic mRNA must undergo a multistep processing before being functional o Called pre mRNA before that Introns are cut out exons are kept through the process of splicing Small nuclear ribonucleoproteins or snRNPs form together to form the spliceosome 5 cap is added as that end emerges from the RNA polymerase o has a modified guanine and three phosphate groups 3 poly A tail is added which is a long row of adenines 100 250 cap and tail protect from ribonucleases which degrade RNA addition of cap and tail are enzyme catalyzed Transcription and translation can both occur in bacteria because the lack of nuclear envelope separating the processes tRNA transfer RNA brings amino acids to ribosomes secondary structure double stranded at some points o CCA sequence on 3 allows amino acid to attach to tRNA o Triplet on a loop serves as anticodon Tertiary structure upside L with anticodon and attachment sites Anticodon set of 3 bases that corresponds to the mRNA Amino acid tRNA attachment Requires enzyme aminoacyl tRNA synthetase o Different one for each of the 20 amino acids Requires ATP endergonic Covalent bond forms aminoacyl tRNA Wobble hypothesis inside a ribosome the 3rd base in the tRNA can wobble to be another base that doesn t follow Watson Crick base pairing thus allowing 40 or so tRNA s to bind to all 60 mRNA codes Ribosome Large and small subunits Small holds mRNA in place Large where peptide bonds form o 3 sites ELONGATION A P E A acceptor or aminoacyl P peptidyl for peptide bonds E exit holds one tRNA that will exit Initiation begins when rRNA section on ribosome binds to a section on the mRNA known as the Shine Dalgarno sequence aka the ribosome binding site o About six nucleotides upstream from the start codon Ribozyme not a protein based enzyme Elongation factors are proteins that help the ribosome move downstream relative to the mRNA Termination release factor recognizes stop codon and fills the A site releasing the polypeptide Control of Gene Expression in Bacteria 01 22 2014 Flow of information DNA mRNA protein activated protein Regulation of Protein Production Transcriptional stop mRNA from being made saves most energy Translational stop after mRNA so proteins aren t made Post Translational stop final proteins from being activated phosphorylation Gene expression is not just on or off The level of expression can vary between both extremes Regulating gene expression allows cells to respond to their environment Finding mutants of a single trait Expose cells to mutagens in random locations on genome Screen cells that have a lack in biochemical pathways associated with this trait Constitutive produces a product at all times Negative control of transcription Repressor regulatory protein o Binds to DNA and stops transcription Positive control Activator regulatory protein o Binds to DNA and triggers transcription o Also binds to RNA polymerase and increases the rate of transcription Repressor is the parking break and lactose releases the break to allow transcription from the DNA Inducer binds to the repressor changing its shape and releasing it Operon set of genes that are transcribed together in one mRNA and are said to regulate the production of proteins Cotranscription coordinated expression of genes that are transcribed together Gene expression is regulated by physical contact between regulatory sites on DNA and regulatory proteins Regulons coordinate expression of different genes on a shared regulon that acts on a regulatory sequence that all share can be negative control or positive control Control of Gene Expression in Eukaryotes 01 22 2014 Levels of control of Gene expression First DNA is wrapped around proteins to make chromatin o The promoter can not contact with the RNA polymerase unless it is released from the tight structure known as chromatin remodeling Second RNA processing o Steps are needed to make a mature mRNA Introns need to be spliced Third mRNA life span is regulated o mRNAs that stay in the cell tend to be translated more
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