GEN 3000- EXAM 3 STUDY GUIDE
GEN 3000- EXAM 3 STUDY GUIDE GEN 3000
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This 8 page Study Guide was uploaded by Jomary Arias on Tuesday March 8, 2016. The Study Guide belongs to GEN 3000 at Clemson University taught by Dr. Kate Tsai in Spring 2016. Since its upload, it has received 116 views. For similar materials see Genetics in Biomedical Sciences at Clemson University.
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Date Created: 03/08/16
GEN 3000 EXAM 3 STUDY GUIDE EXAM 3 STUDY GUIDE CHAPTER 9 Key Terms DNA is made up of units of 4 bases in a fixed sequence DNA vs Protein as a means of encoding information composed of nucleotides that consist of a phosphate sugar and nitrogenous base Sugar Base contains Oxygen Sugar Base does NOT contain Oxygen gives DNA it s negative charge and makes acidic substance A T G C the amount of time it takes for hydrogen bonds to renature into a double stranded helix after being denatured using heat Important People Levene proposed tetranucleotide theory Nucleotides are the most basic components of DNA made of sugar phosphate and base Miescher studied the medical relevance of puss and discovered nuclin DNA in the nuclei of WBC Kossel determines that DNA contains nitrogenous bases known as Adenine A Thymine T Guanine G and Cytosine C There is an equal relationship between bases since they re xed and paired Griffth demonstrates the transforming principleearly efforts to ID Used Streptococcus Pneumonia and identified two strains 1 Virulent Strain has polysaccharide coat smooth 2 R Strain DO Not have polysaccharide coat rough Some R strains could spontaneously become smooth Hershey and Chase demonstrates that DNA is genetic material in viruses Avery MacLeod amp McCarty demonstrated that DNA is the genetic material in bacteria Isolated transforming principle Chargaff isolated DNA and found varied in composition Xray crystallography was key to unlocking DNA structure xrays are beamed at crystal sample and hit detector photographic plate resulting in a diffraction pattern GEN 3000 EXAM 3 STUDY GUIDE 0 Watson amp Crick used chemistry amp Xray diffraction to solve DNA structure Solved B DNA Properties of Genetic Material 1 Must be capable of being replicated faithfully 2 Must encode amp store complex info 3 Must contain enough info To yield phenotype 4 Must have variation as result of mutation yields various phenotypes because of different alleles Includes Adenine A and Guanine G Includes Cytosine C Thymine T and Uracil U DNA Structure Watson amp Crick gt Pyrimidine Pyrimidine DNA too Thin Small in size Small gt Purine Purine DNA too thick Large Large gt Purine Pyrimidine DNA thickness compatible With Xray data DNA polynucleotide strand RNA polynucleotide strand Contains Sugar Phosphate backbone Contains Sugar Phosphate back bone Strands run in opposite directions Generally single stranded Antiparallel Thymine is switched for Uracil 3 types of DNA A Form B Form Z form Alpha heliX Alpha heliX RIGHT LEFT handed heliX Shorter amp Wider spiral Zigzag backbone Probably does NOT 10 bp per rotation Sites of active genes exist in nature Exists in the presence can make Z DNA of water Most stable of DNA s under physiological conditions Alpha heliX GEN 3000 EXAM 3 STUDY GUIDE Key Terms 0 Primarv Structure nucleotide sequence AT GC 0 Secondarv Structure double stranded helix 0 Tertiarv Structure higher order packing 0 Super coiling either adding more spins over rotating or unraveling DNA and taking away spins under rotation 0 Positive Supercoil add rotations 0 Egative Supercoil remove rotations 0 Chromatin complex of DNA and proteins in eukaryotic chromosomes contain histones 0 Scaffolding Proteins nonhistone play a role in folding and packing 0 Nuclease cuts DNA resulting in multiple fragments identical in size 0 Linker DNA combines core histones of nucleosome to chromatin known as beadson astring 0 Nucleosome two copies of H2A H2B H3 and H4 DNA o Histone tails targets for binding 0 Acetylation neutralizes positive charge and relaxes histone hold 0 Methvlation and phosphorvlation gives the histone hold strength and becomes heterochromatin o Polytene Puff region of polytene chromosome that is relaxed and pulled out using chromatin remodeling Allows access to DNA 0 Lampbrush Chromosome mitotic chromosome allows crossing over to take place while the DNA is compacted 0 Centromere region of chromosome where spindle fibers attach 0 CEN region critical for sequences within the centromere region 0 Telomeres maintain ends of chromosomes 0 Transcribed regions TERRA telomeric repeatcontaining RNA contribute to methylation Prokaryotes Most DNA is negatively supercoiled Naked DNA Separation of strands is easier occupies less space than relaxed Bacterial DNA is packaged with proteins not histones Eukaryotes GEN 3000 EXAM 3 STUDY GUIDE DNA always interacting with proteins Half of protein mass is nonhistone chromosomal proteins scaffolding proteins and DNA replication Heterochromatin Euchromatin Highly condensed chromatin inactive X Chromatin can be transcriptionally active EX Teleomere centromere functional DNA known as open chromatin Chromatin Remodeling Structure must change to allow access to DNA allows you to Involves Histone Tails Acetylation Methylation and phosphorylation Remodel histone proteins then use acetylation to allow protein arms to release DNA strand The positive charge of the arms is neutralized by the negatively charged DNA and the arms relax Chromosome Banding Staining of chromosomal regions Helps identify translocations inversions and duplication with in chromosomes Allows us to name areas on the chromosome AT GC Similar to finger prints R banding and Q banding are common types of banding Chromosomes can also be identified by staining the centromere Centromeres Necessary for chromosomal segregation Region of chromosome where spindle fibers attach Without one the chromosome is lost 2 types of centromeres Point centromere Regional centromere Small precise centromere region Very Most plants and animals repetitive within centromere Telomeres Function 1 Structural serves as a cap to blocj unraveling 2 Replication of ends a Generally does not occur to somatic cells because it degrades over multiple round of replication it is shortened to death GEN 3000 EXAM 3 STUDY GUIDE b Singlecelled organism and germ cells do have to deal with this Key Terms Theta Replication can occur with circular DNAs Rolling Circle Replicatio used by some viruses and F factors similar to Theta where is required an origin of replication Linear DNA Replication with Multiple Origins exists on one chromosome to speed up the replication process All Bidirectional but still semiconservative yielding 1 old strand and 1 new strand Replication Fork double stranded DNA splits into single stranded DNA It is antiparallel Topoisomerase can relieve or introduce supercoiling ssDNA binding proteins prevent ss regions from snapping back DNA gyrase topoisomerase located outside and reduces torsional strain that builds as fork moves prevents super coiling by breaking phosodyester bonds Proofreading 3 5 exonuclease removes Termination occurs when 2 forks meet some sequences in some systems bind termination protein and blocks helicase Watson amp Crick created 3 models for DNA replication Conservative Replication Dispersive Replication Semiconservative replication Yields 1 original strand and Old DNA is mixed throughout Conserves a single strand but three new strands the NEW DNA the double stranded molecule gets split apart Chromosome during the second round of replication involve a replication fork in the Interpretation strand Meselson amp Stahl set up tests to identify what type of replication occurs in bacteria Predicted replication occurred through a conservative method After testing the 2quot I generation strands GEN 3000 EXAM 3 STUDY GUIDE ruled out both conservative and dispersive Bacteria replicated in a SEMICONSERVATIVE fashion Replication Requirements 1 ssDNATempIate 2 dNTP s 3 Enzymes Prokaryotes Mechanisms of Replication 1 lnitiation circular chromosome with 1 origin of replication nitiator proteins bind to oriC opening dsDNA Helicase and SSB proteins bind to strand 2 Unwinding occurs through DNA Helicase DNA Helicase enzyme that breaks hydrogen bonds bw the base of strands Located at the fork cannot initiate unwinding without DNA Helicase Priming DNA polymerases cannot initiate DNA synthesisrequire a 3 OH group to extend Synthesizes DNA DNA Pol I has 5 3 polymerase activity building DNA HAS 3 5 exonuclease activity allows correction of errors HAS 5 3 exonuclease activity used to remove primers DNA Pol III large complex has 5 3 polymerase activity has 3 5 exonuclease activity allows correction of errors Primase synthesizes a short oligonucleotide to get DNA replication going Eukaryotic DNA Replication Multiple replications events at the same time on 1 chromosome Large variety of DNA polymerase Nucleosome assembly makes this more of a mess because of the chromatin structure Linear chromosomes that replicate and maintain ends of telomeres P PP N Use Replication Licensing factor which attaches to origin and only then initiator proteins can function GEN 3000 EXAM 3 STUDY GUIDE Key Terms 0 Transcriptional Units stretch of DNA that codes for an RNA molecules amp sequence necessary for its transcription 0 Promotor DNA sequence that transcriptional apparatus recognizes indicates which strand of DNA Will be transcribed determines start site usually not transcribed 0 RNA coding sequence template 0 Terminator stops replication process 0 Sigma factor added to core subunits different sigma factor direct initiation at different promoters o Holoenzymes initiate transcription at promoter Hammerhead Ribozyme catalytic RNA no protein component A11 cellular types of RNA are transcribed from DNA While some Viruses can copy RNA from existing RNA Eukaryotes Prokaryotes amp Prokaryotes Contains many more RNA types Contains Pre messenger RNA pre RNA Messenger RNA mRNA Small nuclear RNA snRNA Ribosomal RNA rRNA Small nucleolar RNA snoRNA Transfer RNA tRNA Micr0RNA miRNA Small interfering RNA siRNA Piwi interacting RNA piRNA How is RNA different from DNA RNA is usually SingleStranded and can acquire a certain shape RNA contains Ribose sugar Ribonucleotides contain the pyrimidine base Uracil instead of Thymine Composed of nucleotides Composed of nucleotides Deoxyribose sugar Ribose sugar No 2 OH group Yes contains 2 OH group Bases AGCT Bases AGC U GEN 3000 EXAM 3 STUDY GUIDE Joined by phosphodiester bonds Joined by phosphodiester bonds Double Stranded Single Stranded Double HeliX Many types of HeliX Stable Easily degraded Transcription Highly selective process only bits of the genome are ever transcribed into RNA Requires 1 ssDNA template 2 Substrates to make RNA Ribonucleoside triphosphates 3 Transcription machinery Bacterial Transcription 3 major stages 1 machinery assembles on promoter begins synthesis of RNA identify promotors 2 RNA polyermerase reads DNA adds ribonucleotide to growing RNA and make RNA transcripts 3 end of transcription separation of RNA from DNA
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