Ch 16 replication Structure of DNA deoxyribonucleic acid o 2 deoxy OH in the ribose o Makes DNA more stable than RNA RNA is subject to hydrolysis 2 OH o Overall structure double helix formed by 2 hydrogen bond antiparallel DNA strands o Components basic unit nucleotides Backbone phosphate group sugar Nitrogenous base purines A G pyrimidine C T U in RNA o A T U 2 Hydrogen bonds o G C 3 hydrogen bonds Enzymes o Replication Helicase unwinds double helix separate two strands o Topoisomerase relieve additional coiling ahead and behind of replication origin o Single stranded binding protein stabilize single strands at DNA helps keep strands separated o Primase adds RNA primer so DNA polymerase can function requires primer o DNA polymerase III 5 prime to 3 prime synthesis of leading strand and lagging strand Proof reading ability o DNA polymerase I fills in RNA primers with DNA o Ligase joins DNA fragments together Errors in replication o Proof reading catches mistakes has an exo nucleic activity so it will go in opposite direction and go and remove the wrong base and add the right base If DNA polymerase doesn t catch this mistake then we have repair enzymes But proof reading catches most mistakes usually o Mismatch repair by repair enzymes o Nucleotide excision repair enzymes remove section of incorrect bases Eukaryotes end replication o We need RNA primer and need to go 5 to 3 Solution is Telomeres repeating sequences of DNA that don t code for anything They just get chopped off are added to ends of chromosomes to prevent shortening Telomeres added telomerase Euchromatin more loosely packed Accessible for transcription Heterochromatin too densely packed to have access to transcription Genes tend to be inaccessible turned off Chromatin double stranded helix DNA wrapped around histones nucleosome complete packing chromatin o Know the diff kinds of histones H2A H2B H3 H4 4 and 4 make an octamere o Histones are positively charged DNA is charged so histone binds tightly to DNA o Folding nucleosome 10 nm fiber 30 nm fiber radial looped domain 300 nm chromatic chromosome o Chromatin is loosely packed in interphase and condenses in mitosis that s when you get your chromosome structure Ch 17 transcription and translation Central dogma flow of genetic information o DNA genetic storehouse Transcription mRNA message translation protein functional Types of RNA o Translation RNA polymerase II o mRNA carries genetic info to be translated into protein o rRNA component of ribosome o tRNA transfers amino acids to growing peptide chain Replication VS Transcription o Both go from 5 to 3 of new strand o Both happen in nucleus in eukaryotes o Both use DNA template DNA DNA replication is replication and DNA RNA is transcription o DNA polymerase requires primer RNA polymerase does not unwinds DNA reads DNA and adds RNA nucleotides so it can synthesize mRNA o RNA polymerase lacks proof reading ability It also has a promoter region in transcription that initiates the binding of RNA polymerase Transcription in Eukaryotes vs Prokaryotes o Prokaryotes DNA mRNA Protein All in cytoplasm No RNA processing Transcription and translation can occur at the same time be coupled o Eukaryotes DNA pre mRNA RNA processing including modifications and splicing coding mRNA exported to cytoplasm protein in cytoplasm Genetic code o Redundant more than 1 codon for same AA o Triplet 1 codon 3 nucleotides 1 AA o Start codon AUG also methionine o Stop codon UAG UAA UGA RNA processing in Eukaryotes o Modifications S cap Poly A tail Helps with transport to cytoplasm prevents degradation helps with binding of ribosome to mRNA o Splicing introns non coding regions not expressed cut out Exons coding regions expressed o Carried out by spliceosomes protein SnRNPs small ribonucleoproteins that recognize splicing sites o RNAs in the spliceosome catalyze splicing ribozymes Translation mRNA Protein o Happens at ribosome with help of tRNA o Ribosome rRNA and protein small and large subunit o tRNA each tRNA has an amino acid binding site for a particular AA tRNA has anticodon which hydrogen bonds to mRNA codon containing complementary sequence Steps of translation o Needs tRNAs with proper AA attached Loading step for tRNAs AA ATP aminoacyl AMP and PPi is gone Aminoacyl AMP tRNA aminacyl tRNA and AMP is gone o o o o o Aminoacyl some AA tRNA its corresponding tRNA Aminoacyl tRNA synthetase is the enzyme Small subunit of ribosome binds to mRNA Small subunit moves along mRNA until it reaches AUG Initiation factors bring large subunit together tRNA s add AA to peptide chain A P E sites on ribosome Termination no tRNA for stop release factor comes in to A site hydrolysis reaction releases protein o Translation is also 5 to 3 along the mRNA o AA amino acids are added at C terminus of protein A site hold tRNA of AA to be added next P site hold tRNA that carries growing peptide chain E site where tRNA s exit o Protein bound for endomembrane system cell membrane ER golgi extracellular lysosome made on ribosome in ER o Signal peptide that are found on these proteins signal if you need to be at the ER and are transported by other proteins Mutations random change in DNA sequence usually bad o Point mutations single base pair substitution Missense 1 amino acid to be replaced by another Nonsense cause stop codon to replace one of the existing codons so you ll have a premature stop Silent change one codon into another codon that will be coding for the same amino acid so no change in the protein o Insertion or deletions cause frame shift mutation way worse than point mutation Ch 18 Operon clusters of genes translated to 1 mRNA and in related metabolic pathways These are all in prokaryotes o Promoter o Operator regulatory site where the repressor binds o Set of genes o Terminator o You can have a co repressor example trp which is a product of the pathway It will inhibit the pathway o Or you can have an inducer ex allolactose substrate molecule o Operons can be repressible or inducible o Trp operon whether to do transcription or not repressible usually on Function is to make tryptophan When trp is absent the repressor is inactive so we make trp When trp is present it binds to the repressor as a co repressor so it activator the repressor The repressor will bind to the operator and its active The operon is off o Lac operon inducible Also regulated by glucose CAP controls the rate of transcription 3 conditions 1 lactose absent turn OFF 2 Lactose present we have
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