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BIOL 302 Week 2/16-2/18

by: Michaela Sanner

BIOL 302 Week 2/16-2/18 BIOL 302

Marketplace > University of South Carolina > Biology > BIOL 302 > BIOL 302 Week 2 16 2 18
Michaela Sanner
GPA 3.5

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About this Document

Cover material covered in class on 2/16/16 and 2/18/16
Cell and Molecular Biology
Erin Connolly
Class Notes
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This 7 page Class Notes was uploaded by Michaela Sanner on Thursday February 11, 2016. The Class Notes belongs to BIOL 302 at University of South Carolina taught by Erin Connolly in Spring 2016. Since its upload, it has received 23 views. For similar materials see Cell and Molecular Biology in Biology at University of South Carolina.

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Date Created: 02/11/16
2/16/16 DNA Repair Mechanisms     ­protect germ + somatic cells      ­all cells have repair mechanisms  DNA Mechanisms      ­fixes errors from replication            1. DNA Polymerase w/o proofreading: 1 in 10^5 nucleotides                2. DNA Polymerase w/ proofreading: 1 in 10^7 nucleotides            3. DNA Polymerase w/ proofreading plus mismatch repair: 1 in 10^9 nucleotides (100  times better) ** DNA mismatch fixes 99% of errors that make it past proofreading Errors in DNA Replication     ­result is a mismatch (structural abnormality)     ­if you repair using new strand as template both molecules have mutation     ­if you repair using parental strand as a template both will be correct **repair system must be able to recognize the new strand           ­>recognize new strand because it has nicks           ­> differences in chemical modifications Steps in Mismatch Repair **Recognize error in new strand     1) removal: of newly synthesized strand in region of mismatch     2) resynthesis: of missing strand               ­>DNA Polymerase fills in gap     3) Ligate: DNA Ligase seals nicks left in sugar­phosphate backbone DNA mismatch repair proteins DNA Damage     ­damage: chemicals, UV light     ­different types of DNA damage           1) Depurination­spontaneous loss of a purine (A,G)                              ­sugar­phosphate backbone is left intact, but base is lost                              ­>often results in a deletion           2) Deamination­spontaneous loss of an amino group (usually loss C­­> U)           3) Thymine Dimer­covalent linkage between 2 adjacent pyrimidine bases (UV radiation exposure)                    ­­> blocks DNA replication **recognition of damaged DNA 1) exasion of damaged DNA     ­leaves small gap 2) resynthesis repair DNA polymerase fills in gap 3) ligate DNA ligase seals nick left in backbone CH 7 Outline How is the info encoded in DNA used to make protein? DNA (replication) ­> transcription­> RNA­> translation­> protein 1) DNA­> RNA 2) mRNA processing 3) mRNA export from nucleus to cytosol 4) RNA ­> proteins Gene expression­­>regulation of the processes Transcription: the copying of one strand of DNA into a complementary RNA sequence by  enzyme RNA polymerase  Genome Facts:     1) DNA molecule­> many RNA copies (amplify genetic info)           ­> some RNAs are very abundant           ­> some RNAs are very rare *regulation­homeostatic mechanisms that ensure proper amounts of each RNA Differences Between DNA & RNA DNA                              RNA      deoxyribose                    ribose ACGT                              ACGU double­stranded               single­stranded overall structure of RNA is different from DNA     ­RNA molecules tend to fold up into a variety of different shapes     ­RNA can form intramolecular base pairs           ­short stretches of nucleotides can base pair with complementary stretches found  elsewhere in same molecule                    ­>30 structures                    ­>stem loop structure  Roles in RNA in cells      1) Information carrier     2) structural roles       } ex 2,3 ribose, splicing, tRNA     3) catalytic roles  All RNA is made by transcription (trxn) DNA 5' ATG   CAG   GAT   TAG  3'   sense strand          3' TAC   GTC    CTA   ATC  5'   template strand (anti­sense strand) RNA 5' AUG   CAG    GAU  UAG  3' ­RNA is identical to sense strand (top strand) except u in place of t     ­ribose in place of deoxyribose ­RNA is complementary to template strand (it is made out of template strand) Facts about transcription reaction     ­double stranded DNA molecule     ­enzyme RNA polymerase (DNA dependent, RNA polymerase)          ­catalyzes formation of phosphodiester bones between ribonucleotides Transcription reaction     ­begins with the opening and unwinding of a short stretch of DNA (exposes bases_     ­only 1 of 2 strands is used as a template     ­nucleotide sequence of RNA is determined by complementary base­pairing of incoming  ribonucleotides on DNA template     ­RNA synthesis proceeds 5'­­>3' end adds ribonucleotides at 3' end of a chain     ­ATP, CTP, GTP, UTP     ­RNA is a chain of ribonucleotides (transcript) 2/18/16 Differences Transcription and DNA ­Transcription is conservative process         ­**parental DNA helix is preserved  ­RNA molecules are much shorter than DNA molecules         Ex: human chromosome ~250million nucleotide pairs long                                                  ~RNA molecule few thousand nucleotides long ­may see many RNA polymerases on a single stretch of DNA at one time         ~1000 transcripts per gene per hour RNA polymerase (versus DNA polymerase)         ­adds ribonucleotides         ­no primer needed         ­no proofreading                  ­transcription is not as accurate as DNA replication; error rates:                          1 in 10^4­10^5 nucleotide transcription and                         1 in 10^7 nucleotide replication and proofreading and                          1 in 10^9 replication+proofreading+mismatch repair *Not all RNAs are the same         1) mRNA (messenger RNA)                  ­code for protein    **other RNAs: final product is RNA (non­coding RNAs)          2) rRNAs (ribosome RNA)                 ­form core of ribosome          3) tRNAs (transfer RNA)                 ­translation, form the adapters that select an amino acid hold them in place on  ribosome for incorporation into a new polypeptide chain          4) small RNAs                  ­splicing, gene regulation (micro RNAs, siRNAs)  Transcription in Eukaryotes         v                Prokaryotes                         ­3 RNA polymerases             ­1 RNA polymerase                         ­each RNA carries info          ­a set of a adjacent genes transcribed as a unit                          from single gene.                   (Transcript is one strand to form RNA (Operon­ set of                         (transcript is 3 segments.       Genes transcribed as unit) then 3 separate  proteins)                         To form RNA and 3 separate                         Proteins; no operons)                          3 RNA Polymerases in Eurkaryotes         RNA polymerase 1­­> involved in synthesis of most rRNA         RNA polymerase 2­­> involved in synthesis of most mRNA and some small RNAs         RNA polymerase 3­­> involved in synthesis of most tRNAs and some rRNAs and some  small RNA Transcription          1) Initiation          2) Elongation.            } a) prokaryotes          3) Termination.             b) eukaryotes Transcription in Prokaryotes         ­Promotor ­ nucleotide sequence in DNA to which RNA polymerase binds to begin  transcription                 ­­>correctly orients RNA Polymerase on DNA          ­RNA Polymerase ­ special subunit in prokaryotes                                                  ­sigma factor (s.f) is important for transcription initiation                                                          ­recognizes the Promotor          Steps in Transcription in Prokaryotes                 1) RNA polymerase with sigma factor binds weakly to DNA                  2) slides along double stranded DNA until it reaches Promotor (transcription  initiation site)                         ­Promotor has ­35 to ­10 pribnow box                  3) opens up helix                  4) exposes the nucleotides on the template for RNA synthesis                                  ­­> RNA polymerase then synthesizes a short (~10 nucleotide long)  RNA                                  ­­> sigma factor no longer needed falls off (dissociates from complex)                 5) RNA polymerase synthesis RNA until it reaches a terminator sequence                  6) RNA Polymerase will fall off DNA and may reassociate with sigma factor and  start process again Transcription in Eukaryotes          Eukaryotic Transcription Initiation                 3 basic requirements                         1) RNA polymerase (RNA polymerase 2)                          2) general transcription factors                         3) Promotor element TATA box (region of the Promotor) (rich in T and A)                                  ­specific DNA sequence                   RNA Polymerase 2 and the General Transcription Factors (T.F)         ­"General" because they assemble at all promotors transcribed by RNA polymerase 2                 1) help position RNA polymerase 2 correctly at the Promotor                  2) help RNA polymerase 2 to pull apart 2 DNA strands                  3) help RNA Polymerase 2 to leave Promotor as transcription begins  TATA Box         ­DNA sequence composed of adenine and thymine          ­found in promoters of most eukaryotic genes that are transcribed by RNA polymerase  2         ­specifies where transcription begins          ~25 base pairs upstream (­25) of transcription start site  Transcription Initiation in Eukaryotes ­Mechanism          ­assembly of general transcription factors on the Promotor (RNA polymerase 2)***                 1) Binding of TF II D (General Transcription Factor) to the TATA Box                         (TF II D­ Transcription Factor II because RNA polymerase 2 D)                          ­TF II D­ has a subunit called TBP                          ­TBP­ TATA Binding Protein                          ­TBP binds to the TATA box and causes DNA to bend                          ­bending of the DNA attracts (recruits) other general transcription factors                  2) Binding of TF II B                  3) Binding of TF II E, TF II F, and TF II H and binding of RNA polymerase 2                         **complete transcription initiation complex **                 4) TF II H uses ATP to pry apart the DNA double helix                          ­>TF II H Helicase activity                          ­> this allows transcription to begin 


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