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Biology 1002 Outcomes Midterm 2.pdf

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Department
Biology
Course
Biology 1002B
Professor
Tom Haffie
Semester
Fall

Description
Overall Themes - 2nd half February 12, 2013 9:42 PM Prokaryoticenvironmentvs Eukaryotic environment What's the information in DNA? • Protein-coding information • RNA-coding information • Codons - specify amino acids ○ Start codon - AUG ○ Stop codons - UAA, UAG, UGA ○ Trp codon - UGG • Promoter- attracts the attention of RNA polymeraise • UTR (untranslated region) - stretch of DNA between Promotersegment and start codon. ○ Transcribed into RNA, but NOT translated because it's 'upstream' of the start codon' • SD Box (located in the UTR) - helps the initiation of translation (in bacteria) by complementary base pairing before the start codon • Operator - regulatory DNA sequence in the operon; binding sequence for a regulatory protein. • Enhansers - proteins bind to enhanse transcription levels of genes in a gene cluster, eukaryotesonly? • TATA box - region where TATA binding protein is bound to the promoterattracts RNA polymeraiseand other transcription factors • Peptide tag - aminoacid sequence that tells the cell where the RNA should go from the chloroplast (i.e. to the; ER, nucleus, chloroplast) ○ This sequence appers in the coding region of the DNA How to get information out of DNA • RNA polymerase - itentifies and transcribes genes • Ribosomes - assemblesproteins from • Operons ○ Repressor (regulatory protein); when bound to DNA, reduces the likelyhoodthat genes will be transcribed ○ Activator ( regulatory protein); when bound to DNA, increases the likelyhood that genes will be transcribed • Promoters - • Enhansers - • Regulating enhansers/promoters= different expression of genes (by binding proteins onto them) • Eukaryotes - 5' phosphate cap - recognized by the small ribosomalsubunit and begins the ribosomescanning along the mRNA Examples of the importance of complementary basepairing: • mRNA pairs with itself • tRNA pairs with itself • In DNA structure • In Transcription • SD box • snRNApairs with itself • ALL RNAs PAIR WITH THEMSELVES • - & snRNPs Stop Codon vs Termination Sequence • Stop codon signals the end of translation by the ribosome • Stop codon signals the end of translation by the ribosome • Terminatorsequence base pairs with itself into a hairpin structure to stop RNA polymeraiseby dissassociating the mRNA sequence, causing it to 'fall off' ○ Terminatorsequenc is located after the stop codon How to Study • Make pictures of genes showing the relative location of signals • Make a chart of signals and how they are understood ○ Release factor in the ribosome - is always competetingto ge into the ribosome,but while translation is happening, it's out competedby tRNA (which binds more readily)  Is a PROTEIN, does not base pair. • Make a list of RNA functions ○ Xist-Tsix regulation (non-coding RNAs regulating gene expression) • Make a diagram of gene expression that highlights complementarybase pairing • Make a chart comparing proks to euks This picture is important Transcriptional regulation Determines Chromatin •Regulation  of  transcription  initiation   which genes •Chromatin  remodeling  to  make  genes   are transcribed accessible for transcription pre-mRNA Posttranscriptional regulation Determines •Variations  in  pre-mRNA processing types and •Removal  of  masking  proteins   availability of •Variations  in  rate  of  mRNA  breakdown   mRNAs to ribosomes •RNA  interference • Mature RNAs Ribosome Translational regulation Determines rate •Variations  in  rate  of  initiation  of  proteat which proteins synthesis are made New polypeptide chains Posttranslational regulation Determines Finished proteins •Variations  in  rate  of  protein  processing  availability •Removal  of  masking  segments   of finished •Variations  in  rate  of  protein  breakdown proteins Protein breakdown Fig. 14.6, p. 316 In general, the  location  of  different  types  of  information  coded  in  DNA  and  how  is  each  one  “understood”  by   the cell how prokaryoticgene structure/expressionis different than eukaryotic role of various types of RNA in gene expression role of complementarybase pairing in gene expression likely effect of mutations in various DNA signals Lec 11 - Intro to prokaryotic Gene Structure February 12, 2013 9:43 PM Lecture Outcomes • relative sizes of typical mitochondrial, chloroplast and nuclear genomes Nucleus - 120 00 kilobases Mitochondrial - 16 kilobases Chloroplast - 200 kilobases • rubisco structure and assembly from componentscoded by different genomes • possible reasons why modern organelle genomeshave become dramatically smaller over evolutionarytime ○ Evolvedto be very specific - only carry out specific processes ○ Some redundant genes have been deleted  Mutation/deletion  Lateral gene transfer - transfer to the nucleus □ Redundant genes:  Flagella, movementgenes  Hexokinease,glycolysis genes not needed in organelles ○ Mitochondria with smaller genomes may have had selective advantage because they'd be easier to replicate. • possible reasons why genes have movedto the nucleus from organelles over evolutionary time So the nucleus can have more control - coordinated control So that the cell won't reject the cell So  that  oxygen  (  produced  in  this  cell)  doesn’t  react  with  important  genes  - causes mutations and damage. Nuclear DNA can undergo sexual reproduction, which generates genetic diversity (positive) • possible reasons why certain genes have not movedto the nucleus from organelles ○ Genes in the organell need local control - need to be inside in order to sense problems ○ Too hard to transport proteins and products from those genes from the cytosolinto the organelle ○ Too big to move - structure just doesn't work in the nucleus. ○ Environmentin organelles in prokaryotic [vs eukaryoticenvironmentin the cell]  Difference in these environments - something has to change ○ Just Chance - genetic drift; hasn't been enough time for them to move over • basic mechanism of transcription and translation in prokaryoticorganelles vs. eukaryotic nuclear environments • basic structure and function of RNA polymeraseand ribosome ○ RNA polymeraseitentifies and transcribes genes - including it's own  Basic protein structure (amino acid chains etc.) ○ Ribosomes are primarily made up of RNA ( the catilytic part) and then protein (the structiral part)  Are responsible for assembling the proteins of the cell • examples of complementarybase pairing in gene expression ○ RNA pairs with itself ( complementarybase pairing)  tRNA pairs withself inorder to obtain proper strcture  RibosomalRNA basepairs with itself to achieve 3D structure inorder to be catalytic. Lec 12 - Prokaryotic Gene Function Reviewing Chapter 13, Gene structureand expression. Focus on prokaryoticgenes February 13, 2013 3:22 AM Independent Study Outcomes 1. identify the sequence of standard "start" and "stop" codons a. Start: AUG b. Stop: UAA, UAG, UGA 2. identify the function of "start" and "stop" codons a. Start: The first codon read in an mRNA in translation b. Stop: A codon that does not specify amino acids - AKA nonsense codons. 3. compare the overall gene expression of prokaryotic vs. eukaryotic cells. a. The same codons specify for the same amino acids in all living organisms and even viruses (with some exceptions) Lecture Outcomes • relative  location  of  such  DNA  sequence  “signals”  as  promoter,  5’  and  3’  UTR,  “SD  box”,  start  codon,  stop  codon,   transcription terminator etc. ○ 5' to 3', the order of things in the DNA:  Promoter  UTR (untranslated region) - AKA, the SD box  Start Codon  Gene(s)  Stop Codon  Transcription terminator • mechanism by which each signal is interpreted, or understood, by the cell ○ Promoter - attracts the attention of RNA polymerase ○ UTR (Untranslated Region) - Transcribed into RNA, but NOT translated because it's 'upstream' of the start codon'  Is the first region transcribed  tRNA doesn't pair with UTR □ SD Box (part of the UTR)- In bacteria, rRNA (ribosomal RNA) pairs with it to help the initiation of translation ○ Startcodon - starts translation by the ribosome  Not the first 3 bases transcribed (that's the UTR) ○ Genes - transcribed by DNA polymeraise, translated by ribosomes into proteins. Three major stages of translation: □ Initiation: translation components assemble on the start codon of the mRNA □ Elongation: the assembled complex reads the string of codons in the mRNA one at a time, while joining the specified amino acids into the polypeptide □ Termination: completes the translation process when the complex disassembles after the last amino acid of the polypeptide (specified by the mRNA) has been added ○ Stop Codon - stops translation by the ribosome ○ Transcription terminator - is transcribed by the RNA polymerase, base pairs with itself and creates a 'hairpin loop' this tells the RNA polymerase to stop.  Destabilises mRNA still bound to the DNA (by base pairing) such that mRNA falls off  Only understood as RNA • relationship between DNA sequence of signals and their function (ie. how would low efficiency promoters be different than high efficiency promoters? • characteristics of promoters that require a particular position and direction ○ When polymeraise binds onto a promoter they have to go 3' to 5'  i.e Where ever the start codon is, is the way it must travel. • change in amino acid coded, given a change in the DNA sequence (and Genetic Code table) ○ WTF DOES THAT EVEN MEAN. DO YOU EVEN GRAMMAR, HAFFIE? ○ A change in the DNA sequence would cause another amino acid to be coded, or the same one to be coded or a sequence for Start or Stop? • base sequence of start and stop codons as mRNA and DNA ○ Start:  mRNA: AUG  DNA: TAC ○ Stop:  mRNA: UAA, UAG, UGA  DNA: ATT, ATC, ACT • the location of various signals given a diagram of gene expression promoter startcodon Stop codon Outcomes Midterm 2 Page 4 Transcription SDbox terminator Outcomes Midterm 2 Page 5 Lec 13 - Prokaryotic Gene Regulation Reviewing Chapter 14, Control of gene expression; especially the Sections 14.1a and 14.1b. February 25, 2013 2:14 AM Independent Study Outcomes 1. identify the main features of bacterial operons ○ Operon - a cluster of prokaryotic genes & DNA sequences involved in their regulation ○ Operator - regulatory DNA sequence in the operon; binding sequence for a regulatory protein.  Repressor (regulatory protein); when bound to DNA, reduces the likelyhood that genes will be transcribed  Activator ( regulatory protein); when bound to DNA, increases the likelyhood that genes will be transcribed ○ Transcription unit - cluster of genes transcribed into a single mRNA (operon transcribed as a unit from the promoter) 2. identify the function of repressor proteins ○ Repressor (regulatory protein); when bound to DNA, reduces the likelyhood that genes will be transcribed  This is because it blocks RNA polyerase from binding to the promoter  Sometimes it slips off 3. identify location of various components of the lac operon (In order:) ○ Regulatory gene - encodes lac repressor ○ Promoter - binds RNA polymerase ○ Operator - binds Lac Repressor ○ lacZ - gene; encodes for the enzyme B-Glactosidase ○ lacY- encodes a permease enzyme that transports lactose actively into the cell ○ LacA - encodes a transacetylase enzyme (relevant to metabolism of compounds other than lactose) Lecture Outcomes • DNA signals in RNA-coding genes (see first part of lec 12 outcomes) • DNA sequence of anticodon in tRNA gene, given the codon ○ UGG on the mRNA,ACC on the tRNA • likely effect of base sequence substitutions in various DNA signals ○ Promoter:  Can't recognise the gene  Might inhibit polymeraise binding  Could increase it's effeciency  (can have bothe positive and negative effects) ○ SD Box:  Effect on the effecency of translation (more or less) ○ Start Codon:  You can break it. - destroys it and kills the gene ○ Stop Codon:  If you destroy the stop codon; the ribosome won't stop translation □ It  will  continue  to  read  through,  and  won’t  stop  until  it  reaches  another  stop  codom □ Often we find redundant stop codons ○ Transcription Terminator:  Changes its effeciency (works better or worse) • change in amino acid coded, given a change in the DNA sequence (and Genetic Code table) ○ Silent mutations  Codon changed for another of the same amino acid ○ Missense mutations - mutated basepair from a normal  Changes the gene into a different codon ○ Nosense muatations  Changes the gene ○ Indel mutations - fairly severe; insertion of a base pair  Disrupts reading frame downstream - new set of amino acids • base sequence of start and stop codons as mRNA and DNA • base sequence of start and stop codons as mRNA and DNA • the location of various signals given a diagram of gene expression • basic structure of lac operon Regulatory gene Transcription unit of three structural genes lacI lacZ lacY lacA Promoter Operator DNA ○ Transcription termination site initiation site Lac repressor β-Galactosidase Permease Transacetylase RNA polymerase • mechanism of action of lac repressor ○ Functions as a dimer (binds as a dimer) - loops out the promoter so the RNA polymeraise can't get past the loop. • function of lac operon in the presence, and absence, of lactose In the absence of lactose, lac repressor binds to operator and prevents transcription In the presence of lactose - allolactose (an inducer and isomer of lactose) changes the repressor's shape so that it can no longer bind to the operator and prevent ranscription • possible location of mutations in lac operon that give rise to a given phenotype • phenotype that would arise from a given mutation in lac operon under given conditions Reviewing sections relating to eukaryotic gene structure and Lec 14 - Eukaryotic Genes function: 13.4 and 14.2, 14.3. In particular, see Fig. 13.19 and February 27, 2013 14.15. As usual, watch the "Concept Fixes". 1:40 AM Lecture Outcomes • basic structure of eukaryotic vs prokaryotic cell with respect to gene expression Eukaryotes Prokaryotes Ribosomes initially away from mRNA (because of the nuclear membrane, allows for more Ribosomes attach to mRNA even as mRNA is still being oppurtunity for gene regulation transcribed from the nucleus •Transcription Control •Post-Transcriptional Control •Translational Control •Post-Tranlational Control Nuclear gene structure is more complicated Promoter only •Promoter proximal region + p
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