Ch 16: replication- Structure of DNA: deoxyribonucleic acido 2- deoxy OH in the riboseo Makes DNA more stable than RNA, RNA is subject to hydrolysis @ 2 -OHo Overall structure: double helix formed by 2 hydrogen bond anti-parallel DNA strandso 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 bondso G-C 3 hydrogen bonds- Enzymes:o Replication Helicase: unwinds double helix/separate two strandso Topoisomerase: relieve additional coiling ahead and behind of replication origin o Single-stranded binding protein: stabilize single strands at DNA, helps keep strands separatedo 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 abilityo DNA polymerase I: fills in RNA primers with DNAo Ligase: joins DNA fragments together. - Errors in replication:o Proof reading catches mistakes: has an exo-nucleic activity so it will goin 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/chromosomeo 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 strando Both happen in nucleus in eukaryoteso Both use DNA template: DNA -> DNA replication is replication and DNA-> RNA is transcriptiono DNA polymerase requires primer; RNA polymerase does not (unwindsDNA, 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 -> Proteino Happens at ribosome with help of tRNAo 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. Aminoacyl (some AA)-tRNA (its corresponding tRNA). Aminoacyl-tRNA synthetase is the enzyme o Small subunit of ribosome binds to mRNAo Small subunit moves along mRNA until it reaches AUGo Initiation factors bring large subunit togethero tRNA’s add AA to peptide chain. A->P->E sites on ribosomeo 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 mRNAo 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 beat 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 codingfor the same amino acid, so no change in the protein. o Insertion or deletions: cause frame shift mutation, way worse than point mutationCh 18- Operon: clusters of genes translated to 1 mRNA and in related metabolic pathways. These are all in prokaryotes: o Promotero 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,
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