Bio 2 Final Notes Chapter 15 DNA and the Gene Synthesis and Repair Semiconservative DNA replication the parental strands of separated DNA act as a template for the synthesis of a new daughter strand Resulting strand has 1 old strand and 1 new strand Bidirectional replication bubbles form in 2 directions during replication DNA Polymerase enzyme that polymerizes deoxyribonucleotides into DNA catalyzes DNA synthesis only work in 1 direction can only add deoxyribonucleotides to 3 end of growing DNA chain DNA synthesis always proceeds in 5 3 direction require a primer to begin synthesis Origin of Replication the replication bubble formed at a specific sequence of bases bacterial chromosomes only have 1 OoR replication fork Eukaryotes have multiple OoR 2 replication forks each Generally very rich in A T fewer H bonds easier to pull apart Replication Fork Y shaped region where the parent DNA double helix is split into 2 single strands and copied DNA Helicase enzyme that breaks H bonds b w base pairs each rep fork has 1 pulls strands apart Single strand DNA binding proteins SSBPs molecules to prevent bases from reattaching and reforming double helix Topoisomerase enzyme that cuts DNA allows it to unwind and rejoins it ahead of the advancing replication fork to relieve stress of pulling force in double helix nick one Phosphodiester bond to relieve stress Primer a RNA strand a few nucleotides long that is bonded to the template strand provides DNA polymerase with a free 3 hydroxyl OH group that can combine with an incoming deoxyribonucleotide to form a Phosphodiester bond Primase enzyme that synthesizes a short stretch of RNA that acts as a primer for DNA polymerase type of RNA polymerase RNA Polymerase an enzyme that catalyzes the polymerization of Ribonucleotides into RNA doesn t require a primer to begin synthesis Sliding Clamp holds the DNA polymerase in place on the template strand during strand extension Leading Strand enzyme s product that leads into the replication fork and is synthesized continuously Lagging Strand lags behind the synthesis occurring at the fork as the rep fork moves it exposes gaps of single stranded template DNA Okazaki Fragments short DNA fragments produced during replication of the lagging strand template DNA Ligase enzyme that joins pieces of DNA by building Phosphodiester bonds b w the pieces on the backbone Summary DNA synthesis begins at specific OoR on the chromosome and proceeds in both directions Synthesis at the rep fork occurs in 3 steps 1 helicase opens the double helix SSBPs stabilize the exposed single strands and topoisomerase prevents twists downstream of the fork 2 DNA polymerase synthesizes the leading strand after primase has added an RNA primer 3 A series of enzymes synthesize the lagging strand Lagging strand synthesis can t be continuous bc it moves away from the rep fork In bacteria primase DNA polymerase and ligase work in sequence to synthesize Okazaki fragments and link them into a continuous whole Telomere repeating sequences at the end of chromosome can afford to lose some of them finishes the shortened lagging strand and extends the unreplicated end don t contain genes Telomerase enzyme that catalyzes the synthesis of DNA from an RNA template that it contains adds DNA onto the end of a chromosome to prevent it from getting shorter only found in cells that produce gametes not somatic cells chromosome of somatic cells gradually shorten as cell become older in cancer cells Correcting Mistakes in DNA Synthesis DNA polymerase can proofread Mismatch repair occurs when mismatched bases are corrected after DNA synthesis is complete Chapter 17 Transcription RNA Processing and Translation Transcription the process that uses DNA template to produce a complementary RNA Template strand strand that is read by the enzyme 1 Initiation Promoter where the work begins initiates transcription Eukayotic promoter TATA box Spacing of TATA box and start codon is critical Upstream of mRNA Recruits proteins tells them where to start and which direction to go Double stranded sequence that marks where to start Worker RNA polymerase Terminator where the work is stopped Read by Polymerase template strand noncoding strand antisense strand Made by polymerase non template strand coding strand sense strand Basal Transcription Factors proteins in eukaryotes that assemble at promoter and RNA polymerase follows 2 Elongation RNA polymerase adds nucleotides to the 3 end of growing RNA strand doesn t have to complete its work before a 2nd RNA polymerase starts working 3 Termination RNA polymerase transcribes a terminator sequence and keeps going in eventually the RNA molecule will be cut free from the polymerase just past this eukaryotes terminator varies slightly RNA Processing translated into a protein mRNA In bacteria when transcription terminates the result is a mature mRNA that s ready to be In Eukaryotic genes are transcribed the initial product is a primary transcript pre Exons expressed regions of eukaryotic genes that are part of the final mRNA Inrons interrupt Spliceosome complexes of proteins and folded mRNA cut out introns regions of eukaryotic genes that cut out of final RNA product snRNPs cut out introns make up spliceosome 5 cap and poly A tail added to pre mRNA after splicing which now becomes mature mRNA ready to be translated sent out of nucleus into cytoplasm Translation when a polypeptide is synthesized from info in codons of mRNA Ribosome built out of 2 subunits large where peptide bond formation takes place and small holds mRNA in place during translation 3 mRNA binding sites A arrival site E exit site P peptide binding site synthesizes proteins Transfer RNA tRNA amino acids are transferred from the RNA to a growing polypeptide Anticodon a set of 3 ribonucleotides that forms base pairs with the mRNA codon Wobble theory many amino acids are specified by more than 1 codon codons for the same amino acid tend to have the same nucleotides at the 1st and 2nd positions but different nucleotide at the 3rd position Chapter 18 Control of Gene Expression in Bacteria DNA transcription mRNA translation protein post translational modifications activated protein Transcriptional control efficient saves most energy but slow Translational control allows cell to make rapid changes Post translational control most rapid response fast but energetically expensive Operons a region of prokaryotic DNA that codes for a series of functionally related genes and is transcribed
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