Exam 2 Study Guide
Exam 2 Study Guide BIOL-L211 2521
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This 14 page Study Guide was uploaded by AnnaClippinger on Tuesday October 20, 2015. The Study Guide belongs to BIOL-L211 2521 at Indiana University taught by Megan Dunn in Summer 2015. Since its upload, it has received 272 views. For similar materials see Molecular Biology in Biology at Indiana University.
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Date Created: 10/20/15
BIO 211 EXAM 2 STUDY GUIDE 0 Go over the T2T questions and answers 0 Go over the diagrams and images in notes 0 Go over the Molecular Biology in the News readings 4 o Read the readings in the textbook 0 Go over the weekly review session questions and answers 0 Review problem set 2 questions and answers 0 Go through the lecture notes and make sure to know all of the topics that she reviewed heavily and talked about the most 0 Review the previous study guide just incase some of the material is on the exam some of this material will build off of previous material 928 KEY TERMS Mitochondrial Transplantation a mitochondria with mutated DNA is denucleated removal of the nucleus and the nucleus from the mitochondria with the mutated DNA is then inserted into a mitochondria with normal DNA that has its nucleus removed to create a hybrid egg to be fertilized Fertilization 100 O C O a O fvlrtochoncirral l myopathy NLiClDLIS DIORPd O a normal denucleated egg ATP synthase particles inler membrane space Matrix 0 o l o 0 O a o 0 gt g Q Normal O C E 0 O Wquot 39 O a 39 Mitochondria wrih mutated DNA Innermembrane Denucleanon 0 Normal mitochondria Ouler membrane cristae Ribosome DNA zoom Origin of Replication the point of specific sequence at which DNA replication is initiated Prokaryotic origins of replication single origin of replication can initiate replication more than once per cell cycle and is a known sequence Eukaryotic origins of replication lots 50000 in humans not all used per cell cycle once of the ori used each is activated only ONCE per cell cycle no known consensus sequence a lot harder to define where the origin is since there is no set spot Mutation a permanent change to the DNA heritablesince it s permanent it s passed to your offspring second round replication first round i E a E E lt replication mis I g g g incorporation G T I i 2 2 Z O 2 gt7 W Gain of Function Mutation extremely rare and is a type of mutation that increases or changes protein activity Loss of Function Mutation a random mutation will normally result In a protein s loss of function Point Mutation any alteration in DNA sequence caused by a single nucleotide base change insertion or deletion of a base Substitution the replacement of a single nucleotide with another nucleotide Transition a switch pyrimidine A to pyrimidine G or purine T to purine C Transversion b switch pyrimidine A to purine C or purine T to pyrimidine G a a a a U r4 i Sequence of part ofa Sequence of E 5 normal gene mutated gene Tl a Transition mutation AT to 60 in this example A f DNA 539 3 539 meme 3 b 339 MEWS 5 339 mam 5 b Transversion mutation CG to 60 in this example Insertions a mutation involving the addition of one or more nucleotide pairs to a gene Deletions 1 a deficiency in a chromosome resulting from the loss of a fragment through breakage 2 a mutational loss of one or more nucleotide pairs from a gene 0 Insertions or deletions are due to slippage of DNA polymerase and often occur at repetitive sequences Trinucleotide Repeat Disorder genetic disorders caused by an insertion or deletion of a greater than normal number of trinucleotide repeats repeats of 3 in a specific gene Mismatch Repair System the cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides immediately following the replication machinery exonuclease i 3 I D 539 gt gt gt 1 DNA polymerase 339 T 539 mismatch repaired 2014 Pearson Education inc Dam Methylation the methylation of DNA at 5 GATC3 sequences HemiMethylation when methyl groups are only located on the template strand and not on the newly synthesized strand 1005 KEY TERMS SingleCell Sequencing going in and getting a single cell and comparing it with others and seeing the genetic diversity Aneuploidy a chromosomal aberration in which one or more chromosomes are present in extra copies or are deficient in number Polyploidy a chromosomal alteration in which the organism possesses more than 2 complete chromosome sets it is the result of an accident of cell division Mutagens a chemical or physical agent that interacts with DNA and can cause a mutation BaseExcision Repair System BER the removal and replacement of damaged nucleotide bases recognizes SPECIFIC lesions free 0 uracil H NH normal I X normal 5quot base H N O 5 base fly normal base ll ii i O P H P H P H o I o c 2 O H H o I o 2 O o I o 2 O O I N uracil 0 AP endo cleaves here makes 339OH for Pol I o H N 0 o o I I I I l 0P 0 CH2O Eggs 383 AP 0P 0 CH20 0H AP 0P O CH20 exonuclease cl here site 0 site 0 removes to here i i i oP o CH2 gt oP o CH2 gt oP o cH2 l 0 glycosylase l 0 AP endoexo l 0 O O O 339 3 3 2014 Pearson Education Inc FailSafe Glycosylases scan DNA for bases on newly synthesized DNA that were overlooked by BER failsafe base excision glycosylase repair replication 2014 Pearson Education Inc Nucleotide Excision Repair System NER a repair system that removes and then correctly replaces a damaged segment of DNA using the undamaged strand as a guide does not recognize SPECIFIC lesions distortion DNA polymerase DNA ligase 2014 Pearson Education Inc TranscriptionCoupled Repair expressed genes are scanned by translocating RNA polymerases which detect DNA damage and initiate transcriptioncoupled repair TCR a subpathway of nucleotide excision that removes lesions from the template DNA strands of actively transcribed genes RNA polymerase transcription bubble 5 quotinitializing littuuramamt 339 al lili ll g lllil l i nucleotide excision repair proteins 012074 Pearsm taucalon 39n Error Prone Polymerases a polymerase that guesses which nucleotide base to add and is poorly accurate in doing so Translesion Synthesis substitute DNA polymerases for a different error prone polymerase which will most likely add the wrong base replication stalls at thymine dimers DNA polymerase dissociates and is replaced by errorprone DNA polymerase which guesses which base to add and replicates over the thymine dimer errorprone polymerase is NOT processive and dissociates and is replaced by original DNA polymerase and replication proceeds DNA polymerase III Bclamp POI IV Pol V Din t3or UmuD392C A DNA Photolyase reverses the formation of thymine dimers by physically separating the 2 thymine residues strands UV pyrimidine DNA photolyase light dimer IX b WT ML Jw U l 7 I1 OM Mil l JIM gt 0quot quot39gt yoquot gt Ti UVlight f gt EZD H l 2014 Pearson Education Inc Methyltransferase scans DNA looking for methyl groups and then removes them since methyl groups causes a distortion too small to be recognized by NER NonHomologous End Joining a backup DSB system in some organisms that joins the broken ends of DNA together and there is NO template strand guiding this so it often can result in some mutations as well doubleStrand break in DNA END RECOGNITION BY Ku HETERODIMERS 1 ADDITIONAL PROTEINS l PROCESSING OF DNA ENDS l LIMITED REPAIR SYNTHESIS 1 LIGATION repaired DNA has generally suffered a deletion of nucleotides Homologous Recombination typically the principal pathway used to repair DSB in which homologous chromosomes provide a template for repair Deamination the process by which amino acids are broken down if there is an excess of protein intake removal of the amino group from the amino acid and converted to ammonia the rest of the amino acid is made up of mostly carbon and hydrogen and is recycled or oxidized for energy Oxidation the combination of oxygen with a substance forming oxidea chemical reaction in which there is a loss of electrons or gain or increase in the proportion of oxygen resulting in an increase in oxidation state by a molecule or atom or ion resulting in a mutation AP Site an apyrimidinic or apurinic site that is a location in DNA that has NEITHER a purine nor a pyrimidine base either spontaneously or due to DNA damage mutation Endonuclease an enzyme that cleaves or hydrolyzes phosphodiester bonds within a polynucleotide chain Exonuclease proofreads the DNA and removes improperly basepaired dNTPs only removes the most recent errors Thymine Dimers fusion of 2 thymines caused by UV radiation can cause DNA polymerase to stop during replication and cannot base pair Double Stranded Break one of the most toxic forms of DNA damage break through BOTH phosphodiester bonds and if not repaired the cell will go through apoptosis programmed cell death and results from various forms of radiation physical constraints reactive oxygen species and can also result in deletions 3 SB llironqliom Sandb plmws thoull wile l loinoloqoux DNA f J NUH39llllJiU Mu iolmnnoloqy mul joinioq nudinlml vllcl oinin l lomoloqoux rm omhinahon Lnd JOIHllK b x b t l 0110 sjnt39lml Strand Hlvasmn and l loop formation Holliday Minion H SUlHlIUH Role dIIOH rtsmrt Rewtowd lurk Nature Reviews Cancer Reactive Oxygen Species chemically reactive molecules containing oxygen Superoxide reacts with and damages ALL macromolecules it comes into contact with and the most common target is DNA and can chemically modify bases for cause DSBs Resection exposes small regions of ssDNA a nuclease digests a short stretch of DNA creates ssDNA with 3 tails Microhomology the presence of the same short sequence of bases in different genes Holliday Junction a place where the 2 chromosome strands are going to cross in homologous recombination in order to finish the repair you have to breakresolve the Holliday junctions 0 Branch Migration is the movement of the Hollidayjunction o Heteroduplex DNA is a doublestranded duplex molecule of nucleic acid originated through the genetic recombination of single complementary strands derived from different sources such as different homologous chromosomes DLoop 3 strand invading the homologous chromosome configuration found during DNA replication of chloroplast and mitochondrial chromosomes wherein the origin of replication is different on the 2 strands the first structure formed is a displacement loop or Dloop Transformation the process through which some bacteria take up DNA from the environment 1 the modification of a genome by the external application of DNA from a cell of different genotype Competence a physiological state in which bacteria take up DNA bacteria that are capable of transformation are said to be naturally competent the DNA that the bacteria are taking up is FOREIGN DNA Competent bacteria build the com machinery in the membrane which is composed of at least 40 proteins Ribose the sugar in RNA which has a 2 OH that deoxyribose sugar in DNA lacks NTP Nucleoside Triphosphate what is used in RNA synthesis dNTPs are used in DNA synthesis a molecule containing a nucleoside bound to 3 phosphates a nucleoside is a sugarbase compound that is a nucleotide precursor nucleotides are nucleoside phosphates a nitrogen base linked to a sugar molecule StemLoop Structure aka Hairpin what is formed when short stretches of complementary sequences base pair a lollipopshaped structure formed when a singlestranded nucleic acid molecule loops back on itself to form a complementary double helix stem topped by a loop hairpin single internal A c strands bulge loop UA A I A A C G ACCUL939ACC CGu AG A C G A I u G G A U G G G c A Gc ac G A ltQiyc junction G Internal Loop unpaired nucleotides on either side of the stem Bulge unpaired nucleotide on one side Junctions site where 3 or 4 stems branch off a branch point Transcript the mRNA that is transcribed copy of the gene that tells the ribosomes to make the protein the product of transcription mRNA that acts as a message or a set of instructions for making up protein RNA Polymerase RNAP catalyzes the synthesis or RNA does NOT require a primer uses 1 strand of DNA as template and synthesis occurs in a 5 9 3 direction an enzyme that catalyzes the synthesis of an RNA strand from a DNA template the enzyme that polymerizes RNA by using DNA as a template it can also act as a primase initiating RNA replication site of nucleotide addition to growing RNA strand DNAhdR template strand l I l l I l 39 I I a l39 539 E l 39 I ail47 39 7 quot x 7 39r A 7 Q Ew T l 39Vlquot g V 39quot I 2 39 3 Coding Strand the nontemplate strand the DNA strand with the same sequence as the transcribed mRNA given U in RNA and T in DNA and containing the linear array of codons which interact with anticodons of tRNA during translation to give the primary sequence of a protein Template Strand the DNA strand that forms the template for both the transcribed mRNA and the coding DNA strand Monocistronic an mRNA molecule is said to be monocistronic when it contrains the genetic info to translate only a single protein chain polypeptidethis is the case for most of the eukaryotic mRNAs Polycistronic has multiple genes on it 9 contains genetic info to translate multiple protein chains polypeptidesthis is the case for most of the prokaryotic mRNA Initiation Has 3 steps 1 binding of RNAP to a promoter to a closed complex DNA is doublestranded 2 DNA strands separate to form an open complex strands separate over 3913 bp 3 initial transcriptionpromotor escapeactually REALLY hard to start transcription Elongation Transcription the synthesis of RNA using a DNA template the process whereby RNA is synthesized from a DNA template Has 3 phases 1 initiation 2 elongation 3 termination Promoter Transcription unit E k A M9 39 quot Nontemplate strand otONA 5 r a I I 339 I 39 39 7 RNA nucleotide 3 539 4 RNA Start point DNA 7 polymerase RNA polymerase Olnitiation 339 C Si J51 539 a 339 339 T 539 E l I RNA Template strand Unwound quotan of DNA 539 f gmfsnrztagauyscrlmlon Tempme script 7 strand of DNA QElongation Newlyrnadc RNA Rewound DNA 5 T B 3r 339 339 z z 539 539 1 RNA transcript OTermination 02 Ill 2 Ulquot Completed RNA transcript 1 the transcriptional start site the 1st nucleotide to be transcribed Closed Complex DNA strands still together and closed Open Complex DNA strands separated and open Downstream DNA DNA after the start site 10 Upstream DNA DNA located before the start site promoters Bacterial RNA Polymerase Core consists of 5 subunits 0L39 alpha 1 0L alpha 2 3 beta prime 3 beta and Q omega resembles a crab claw the core catalyzes RNA synthesis and has an active site in the center the 6th subunit is the o sigma factor Sigma 039 Factor determines which promoters RNAP binds to proteins that bind specific promoter sequences and instruct RNAP when to begin transcription 07 quotHousekeepingquot Factor a type of sigma factor that directs transcription of most genes in cells genes with essential or routine function binds to promoters with 35 and 10 regions and the DNA remains in the closed complex Promoter a regulatory region a short distance upstream from the 5 end of a transcription start site that acts as the binding site for RNAP a region of DNA to which RNAP binds in order to initiate transcription 10 and 35 Elements part ofthe promoter and consensus sequences Consensus Sequence the average of all promoter sequences a sequence of nucleotides or amino acids in common between regions of homology in different but related DNA or RNA or protein sequences 1012 KEY TERMS Termination Promoter Consensus Sequence SLIDE 23 OF LECTURE 11 AND SLIDE 4 OF LECTURE 12 EXPLAIN THIS VERY WELL WITH THE DIAGRAM AND ALL Strong Promoter promoter strength is determined by how many transcripts the promoter initiates in a given time and a STRONG promoter has a sequence CLOSER to the consensus Weak Promoter look up lsomerization oZ recognizes and melts the 10 region which produces an open complex is a process called isomerization occurs near 10 region 2 bases in the nontemplate strand flip out insert in pockets within 02 and causes 10 region to be singlestranded promotes further melting 11 Abortive Synthesis RNAP produces and releases numerous short transcripts lt10 bp long Transient Excursion RNAP moves forward to synthesize and release RNA and then retreats along the template lnchworming flexible region allows front of RNAP to move downstream to synthesize and release RNA and then retract Scrunching RNAP remains stationary and bound to promoter as it pulls DNA into itself thought to be the CORRECT model transient excursions RNAP NTPgtn PPon vi M s w 4 l f 39 A i V n 35 10 1 35 10 1 abortive RNA inchworming 35 10 1 35 10 1 abortive RNA scrunching NTPn PPin m i if e AA 39 1 35 10 1 35 10 1 abortive RNA Promoter Escape the interactions are broken between the polymerase promoter and core and sigma factor energy to break the interactions provided by scrunching mechanism Pyrophosphorlytic Editing adds beta and gamma phosphates back on the NTP and is the reverse of the synthesis reaction and then inserts correct ribonucleotide in its place Hydrolytic Editing RNAP backtracks 1 or more nucleotides and cleaves RNA and removes the sequence with error RhoIndependent Termination required formation of a CG rich stemloop and the DNA sequence of a Rho independent terminator is short inverted repeats separated by quot39 AT base pairs followed by a string of T s Terminator Rut Site Rho utilization sites C bases that occur every quot39 12 bases Gene a segment of DNA that codes for a functional product protein Operon multiple genes expressed from a common promoter Flagella massive structures assembles on the exterior of cell contains filaments and they rotates at very high speed to propel the cell body 12 Transcriptional Regulation mechanism by which gene expression is increased or decreased in response to the environment 1019 KEY TERMS Alternative Sigma Factors sigma factors are proteins that bind specific promoter sequences and instruct RNAP where to begin transcription can replace sigma factors with other sigma subunits diff sigma factors recognize diff promoter sequences diff gene sets can be expressed by changing sigma factors a way of coordinately regulating hundreds of genes of similar function throughout the genome LECTURE 13 HAS A LOT OF EXAMPLES sigD used to direct transcription of the promoter for the flagellin gene and flagellin is the protein that is used tobuild the flagellar filament and is NOT in the fIache operon GFP a photoprotein and can be cloned into the genome of an organism to make them emit color FlaChe Operon composed of 32 genes has the promoter PfIache and is expressed via the action of RNAP core and housekeeping sigma factor Transcriptional Fusion fuse a promoter of interest to a reporter gene reporter protein is easily detected not normally present in your research system Activators increase transcription of a gene Repressors decrease transcription of a gene Operator a DNA region at one end of an operon that acts as the binding site for repressor protein a DNA sequence that is recognized by a repressor protein or repressorcorepressor complex when the operator is com plexed with the repressor transcription is prevented Lac Operon dedicated to breaking down lactose into glucose Quorum Sensing quotthe minimal of officers and members of a committee or organization usually a majority who must be present for valid transaction of business Is used by bacteria to communicate with each other by emitting detecting and responding to chemical signals cells indirectly sense their own population density and respond by changes in gene expression Autoinducer an extracellular signaling molecule that is directly sensed by cells and is made by a protein called LuxI Bioluminescence the production and emission of light by a living organism 13 Initiation of DNA replication in E Coli L9 Multiple replication forks DNA polymerase uses an exonuclease to proofread proofreading exonuclease removes improperly basepaired dNTPs Know the repair pathways Know the proteins that are involved with the repair pathways and be able to list their functions Know the resolutions of the strands and the Dloop on Holliday junctions Vertical cutting splicing and gives you DNA strands that are totally reasserted Horizontal cutting patching and gives you some DNA that is exactly the same as the template with no reassortment Difference between exonuclease and endonuclease DNA polymerase uses exonuclease to make repairs Know the different types of mutations Cellular damage mechanisms Transcription and transcription in prokaryotes Examples of prokaryotic gene expression Alternative sigma factors Operons 9 ONLY FOUND IN PROKARYOTES DNA binding proteins and transcriptional regulation 14
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