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BIO 281: Week 3 Lecture Notes & Chapter 3 Notes

by: Andrew Notetaker

BIO 281: Week 3 Lecture Notes & Chapter 3 Notes BIO 281

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These notes cover everything in the lectures from week 3 as well as notes over week 3 readings such as Chapter 12.1, and Chapter 3.
ConceptualApproachBioMajors I
Class Notes
DNA replication. Heredity., mRNA, transcription, RNA. transcription, DNA polymerase, RNApolymerase, discovery Griffith Avery MacLeood McCarty Hershey-Chase structure helix nitrogen bases sugar deoxyribose phosphate purines pyrimidines replication in bacteria oriC DnaA DnaB DnaC DnaG SSB primer polymerase Okazaki topoisomerase ter Tus leading lagging ter




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This 5 page Class Notes was uploaded by Andrew Notetaker on Thursday September 1, 2016. The Class Notes belongs to BIO 281 at Arizona State University taught by Wright in Fall 2015. Since its upload, it has received 28 views. For similar materials see ConceptualApproachBioMajors I in Biology at Arizona State University.


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Date Created: 09/01/16
Week 3 Chapter 3: Life out there Tuesday, August 30, 2016 10:28 AM On the strand of DNA, label the regions you think are hydrophobic/hydrophilic Intermolecularforces of DNA play key roles in shaping the structure, hydrogen bonding And base pair stacking play a crucial role in maintaining the shape of DNA Key point- DNA's structure facilities informationstorage because its highly stable and serves as a templateto replicate itself, but it's probably not the "spark" of life DNA replication can occur because each "parent" strand serves as a template for the synthesis of new "daughter" strands, using base pairing A-T, C-G. DNA polymeraseis responsible for replicating DNA DNA is synthesized in the 3'-5' direction only so that RNA is built from the 5'-3' Key point: DNA replication occurs in the 5'-3' direction because DNA polymerasecan only add incoming nucleotides to the 3' side of the growing strand. The phosphate group from the incoming nucleotide is broken off by the hydroxyl group of the previous nucleotide, creating energy for the reaction. True or False: DNA polymerasewill be able to initiate replication of the template strands: False. DNA polymerasecan't start without a free 3' OH group. RNA primase lays down an RNA primer. DNA polymeraseextends the RNA primer. Lecture 9/1 RNA world hypothesis: many scientists believe that RNA was the original informationstorage moleculein the earliest forms of life. RNA would need to be able to: 1. Serve as a template a. RNA can be complementary alike DNA 2. RNA evolvethe ability to catalyze a simple reaction? a. These results from the 1993 trials should that RNA can catalyze reactions b. RNA could have evolvedthe ability to catalyze reactions over time Initiation of Transcription General transcription factors bind to the promoterand transcriptional activator proteins bind to enhancers. RNA polymerases,unlike DNA polymerases,don’t require primers. Transcription continues until RNA polymeraseencounters a terminatorsequence in the DNA. The newly formed RNA is released. The transcript is synthesized in a 5' to 3' direction RNA polymeraseadds ribonucleotides Notes from the reading: Chapter 12.1 DNA Replication When copying DNA, each individual parent strand serves as a model, or template strand, for the synthesis of a daughter strand. Bio 281 Lecture Page 1 Chapter 12.1 DNA Replication When copying DNA, each individual parent strand serves as a model, or template strand, for the synthesis of a daughter strand. A key prediction of the model is semiconservativereplication. After replication, each new DNA duplex consists of one strand that was originally part of the parental duplex and one newly synthesized stand. Meselson and Stahl found that DNA replicates semi-conservativelyby mixing heavy N DNA 15 with light N DNA. New DNA strands grow by the addition of nucleotides to the 3' end Both daughter strands should grow in length by the addition of nucleotides near the site where parental strands separate, a site called the replication fork. DNA always grows in the 5'-to-3' direction. DNA polymerizationoccurs when the 3' hydroxyl group at the growing end of the polynucleotidechain attacks the triphosphate group at the 5' end of an incoming nucleotide. Two of the phosphates are cleaved to break the high energy bond in the pyrophosphate to drive the polymerizationforward. DNA polymerase catalyzes the reaction and some correct mistakes. Since DNA can only be elongated at the 3' end, the two daughter strands are synthesized in opposite ways. The bottom daughter strand has its 3' end pointed towards the fork and this polymer is long and continuous. This strand is called the leading strand. The top strand starts with its 5' end pointed towards the replication fork, but the strand cannot grow in that direction so as the strand unwinds a new daughter strand will be initiated with every few hundred to few thousand nucleotides. This strand is elongated at the 3' as usual. Each new piece is elongated at the 3' end until it reaches the piece in front of it. This strand is called the lagging strand. The short pieces in the lagging strand are called Ozazaki fragments. Each new DNA strand must being with a short stretch of RNA that serves as a primer. DNA POLYMERASE CANNOT START A NEW STRAND ON IT'S OWN The primer is made by an RNA polymerasecalled RNA primase , which synthesizes a short piece of RNA complementaryto the DNA template. DNA polymerasethen elongates this primer. All new DNA strands have a short stretch of RNA at their 5' end. When the growing fragment comesinto contact with the primer, a different DNA polymerase complex takes over and removesthe RNA primer and continues extending the growing fragment. When the replacementis completed,the fragments are joined by DNA ligase. Along with other proteins and enzymes, topoisomerase II works upstream from the replication fork to relieve stress on the double helix that results from its unwinding at the fork. Helicase separates the strands of the parental double helix at the replication fork. Single-strand binding protein binds to these single-stranded regions to prevent the template strands from coming together. The positioning of the polymerasesis such that both the leading strand and the lagging strand pass through in the same direction, which requires the lagging strand to be looped. Both strands are elongated together and neither outpaces the other. If DNA needs to be repaired, the synthesis slows down for both. DNA polymerase is self-correctingbecause of its proofreading function Most DNA polymerasescan correcttheir own errors in a process called proofreading. On occasion,improper hydrogen bonds form, with the result that in incorrect nucleotide is attached to the new DNA strand. DNA polymerasecan correct these error because it detects mispairing between the template and the most recently added nucleotide. Some errors can slip through proofreading which lead to mutations,which are the ultimate source of genetic variation. Bio 281 Lecture Page 2 attached to the new DNA strand. DNA polymerasecan correct these error because it detects mispairing between the template and the most recently added nucleotide. Some errors can slip through proofreading which lead to mutations,which are the ultimate source of genetic variation. 3.3 Retrieval of genetic information stored in DNA: Transcription Proteins are synthesized on particles called ribosomes. RNA world hypothesis is that RNA was the original information-storagemolecule.Experiments show how RNA could have evolvedthe ability to catalyze a simple reaction. A strand of RNA was synthesized in laboratory and went through different cycles to get the best mutations. RNA is a polymer of nucleotides in which the 5-carbon sugar is ribose The sugar RNA is ribose which carries a hydroxyl group on the 2' carbon. The base uracil in RNA replaces thymine in DNA. RNA is usually much shorter than DNA molecules. In transcription,DNA is used as a template to make complementary RNA As a region of the DNA duplex unwinds, one strand is used as a templatefor the synthesis of an RNA transcript that is complementaryin sequence to the template according to base pairing rules. The enzyme that carries out the polymerizationis known as RNA polymerase, which acts by adding successive nucleotides to the 3' end of the transcript. Only the template strand of DNA is transcribed. Its partner, called nontemplate strand is not transcribed. All nucleic acids are synthesized by addition of nucleotides to the 3' end. They grow in the 5'-3' direction. The DNA and the RNA strand run antiparallel, meaning they run in opposite directions. Transcriptionstarts at a promoter and ends at a terminator The green segments are promoters, regions of typically a few hundred base pairs where RNA polymeraseand associated proteins bind to the DNA duplex. Many eukaryoticand archaeal promoterscontain a sequence similar to 5'-TATAAA-3' which is known as a TATAbox. Transcription continues until the RNA polymeraseencounters a sequence known as the terminator. Transcription does not take place indiscriminately from promotersbut is a regulated process. For genes called housekeeping genes, whose products are needed at all times in all cells, transcription takes place continually. In bacteria, promoterrecognition is mediated by a protein called sigma factor which associates with RNA polymeraseand facilitates its binding to specific promoters. For eukaryotes,transcription requires the combined action of at least six proteins known as general transcriptionfactors that assemble at the promoter. Also needed is the presence of one or more types of transcriptionalactivator protein, each of which binds to a specific DNA sequence known as an enhancer. Once transcriptional activator proteins bind to enhancer DNA sequences, they recruit a mediator complex of proteins, which recruits RNA polymerasecomplex to the promoter. In eukaryotes,the RNA polymerasecomplexresponsible for transcription is called Pol II. Once the mediator complexand Pol II complexare in place, transcription begins and this process is called transcriptional initiation. RNA polymerase adds successivenucleotides to the 3' end of the transcript Once transcriptional initiation takes place, ribonucleotidesare added to the transcript, known as elongation. The RNA polymerase complex is a molecular machine that opens, transcribes, and closes duplex DNA Bio 281 Lecture Page 3 3.4 Fate of the RNA primary transcript The RNA strand that comes off the template DNA is known as the primary transcript. The RNA moleculethat combineswith the ribosometo direct protein synthesis is known as the messenger RNA (mRNA) because it carries the genetic info from DNA to ribosome. For prokaryotes,even as the 3' end of the primary transcript is still being synthesized, ribosomesbind with special sequences near its 5' end and being protein synthesis. Moleculesof mRNA that code for multiple proteins are known as polycistronicmRNA. Primary transcriptsin eukaryotes undergo several types of chemical modification Transcription occurs in the nucleus and translation in the cytoplasmto allow chemical modificationof the primary transcript known as RNA processing. 1. RNA processing consists of three principal types of chemical modification. First, the 5' end of the primary transcript is modified by an addition of a special nucleotide attached by an unsual linkage called the 5' cap, consisting of the modified nucleotide called 7- methylguanosine. This nucleotide bonds backwards by forming a triphosphate bond between the 5' carbon of one and the 3'-OH of the next. This is essential for translation because in eukaryotesthe ribosomerecognizes mRNA by its 5' cap. 2. Next, the primary transcript is modified by polyadenylation, the addition of a string of about 250 consecutive A-bearing ribonucleotides to the 3' end, forming a poly(A) tail. This plays an important role in the export of mRNA into the cytoplasm by stabilizing the transcript. Transcripts in eukaryotesoften contain regions of protein-coding sequence called exons, interspersed with noncoding regions called introns. 3. The third type of modificationis the removalof introns known as RNA splicing which is catalyzed by a complex of RNA and protein known as the spliceosome. The spliceosomebrings a sequence near the 5' end of the intron, (the 5' splice site) and cuts the RNA at this site. The cleaved end connects back on itself forming a loop and a tail called a lariat. The 5' splice site attacks the 3' splice site, cleaving the bond from the transcript and bonding the ends of the exons together. The presence of multiple introns in most genes allow for alternative splicing,allowing for difference ways to yield different mRNAs and different proteins. Some RNA transcriptsare processed differently from protein coding transcriptsand have functions of their own Not all primary transcripts are processed into mRNA, but are processed differently and include important noncoding RNA types such as: • Ribosomal RNA (rRNA), found in ribosomesthat aid translation. In eukaryotes,the genes and transcripts for ribosomalRNA are concentrated in the nucleolus. • Transfer RNA (tRNA) carries individual amino acids for use in translation • Small nuclear RNA (snRNA) found in eukaryotesand involved in splicing, polyadenylationand other processesin the nucleus. Bio 281 Lecture Page 4 polyadenylationand other processesin the nucleus. • Small, regulatory RNA moleculesthat can inhibit translation or cause destruction of an RNA transcript. Two major types of small regulatory RNA are known as microRNA (miRNA)and small interfering RNA (siRNA). Bio 281 Lecture Page 5


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