BSCI222 Dr. Kocher: Test 2 Review Sheet
BSCI222 Dr. Kocher: Test 2 Review Sheet BSCI222
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Date Created: 10/25/15
BSCI222 Review Sheet Test 2 Chapter 8 o chromosomes vary in structure and ploidy 0 structure duplications inversions translocations o ploidy autopolyploids allopolyploids chromosome set manipulation o FISH or fluorescent insitu hybridization is a fluorescent probe on place on telomeres of chromosomes and other sequences that are used to find matching sequences 0 chromosome paints are a mixture of probes used to find different sequences on chromosomes 0 three major types of chromosome mutations o rearrangementextra genes 0 extra chromosomes 0 extra sets 0 duplication is when a segment of the chromosome is duplicated o happens to 1 of genes every million years 0 takes 4 million years for a duplication to be lost 0 around 1000 genes recently duplicated in our genomes o tandem duplication is when the duplicated region is immediately adjacent to the original segment reverse duplication is when the duplication is inverted deletion is when a segment of the chromosome is removed 0 often coincides with duplication one chromosome has two copies of a gene and the other has none 0 can be a result of crossing over 0 if it includes the centromere chromosome won t segregate and will be lost 0 many deletions are lethal can cause imbalances o inversion is when a segment does at 180 degree flip o paracentric inversions that don t include the centromere run parallel to the centromere I meiosis inversion loop recombination causes one chromosome to have multiple copies and 2 centromeres other to have multiple copies but no centromere o pericentric inversions that include the centromere I meiosis inversion loop 2 chromatids have too many copies of some and no copies of others recombinants are nonviable 0 reduce fertility by producing inviable offspring 0 reduce or eliminate recombination within the individual 0 translocation is when a segment of the chromosome moves from one to another nonhomologous chromosome 0 can also move to a different place on the same chromosome 0 reciprocal more common and nonreciprocal o consequences of duplications and deletions 0 change in gene dosage based on presence of genes ex increase when duplicated but lowered when deleted 0 results in over or under expression of genes 0 polytene chromosomes have many strands as opposed to two due to multiple replications without the cell ever dividing 0 many partially condensed strands o puffs are regions of active transcription relaxed o consequences of inversions and translocations 0 change in local gene environment can alter gene 0 differences in chromatin structure 0 may develop abnormalities 0 variation in ploidy is a change in the number of complete chromosome sets 0 haploid is 1N diploid is 2N triploid is 3N often infertile o autopolyploidy arises by nondisjunction with no cell division 0 all sets of chromosomes are from the same set of species 0 double the number of chromosomes 0 happens within an individual can give rise to triploids during meiosis usually partially sterile o allopolyploidy arises by hybridization o chromosome sets are from 2 or more species 0 can happen naturally or synthetically o examples sunflower and modern wheat o nondisjunction at early mitotic division cell doesn t divide 0 creates diploid but fertile gametes during meiosis aneuploidy is when the number of chromosomes is altered pseudodominance is when a normally recessive mutation is expressed haploinsufficient gene is when a single copy of a gene is not sufficient to produce a wild type phenotype position effect is when expression of a gene is altered by its position nullisomy is the loss of both members of a homologous pair of chromosomes 2n2 monosomy is the loss of a single chromosome 2n1 trisomy is the gain of a single chromosomes to have two homologous copies of one chromosome 0 translocation carriers have a robertsonian translocation between chr 21 and 14 do not have down syndrome but have an increased risk of having children with it uniparental disomy is when both chromosomes are inherited from the same parent mosaicism is when regions of tissue have different chromosome constitutions due to mitotic divisions Chapter 9 o e coli have on circular chromosome 0 46 million base pairs which is around 1000 times smaller than the human genome o 4300 genes around 1000 bp per gene plasmids are small circular molecules that are found in bacteria that hold genetic information replica plating is a process where you grow cells on different growth mediums and transport them to different wells in order to isolate specific types of bacteria nutritional mutants o prototrophs can grow on a minimal media salt and carbon source 0 auxotrophs are mutants needs supplements on the media in order to survive because they lost the enzyme to create certain amino acids Lederberg and Tatum used nutritional mutants in order to show that bacteria could exchange genetic material 0 alone they couldn t grow on minimal media but once combined they could transformation is when bacteria take up information from their environment 0 can be dangerous because they don t know where the DNA is coming from 0 once the DNA is inside the cell it lines up with the homologous part of the existing DNA and undergoes two recombination events to allow it to become part of the DNA 0 frequency of cotransformation is inversely proportional to map distance I 10 cotransformation equals 1D map units I rate at which 2 or more genes are transferred to host 0 not efficient most bacteria can t do this need to be electrically treat in lab in order to acquire this ability conjugation is when DNA is transferred from cell to cell through a cytoplasmic bridge 0 needs direct contact to occur which was proved through a Davis UTube Ffactor plasmid has its own mechanism to replicate that allows for conjugation o 100 kb 0 replicates and transfers to a cell that doesn t have an F factor recombines to replace with gene from first bacterium genome 0 rest gets degraded high frequency recombination is when an F factor combines with bacterial genes 0 replicates with rolling circle method transfers to other bacteria 0 leads to increased frequency of recombination of F cell which can change the genotype F is when a F plasmid that was combined with the cell plasmid recombines back out and takes some bacterial chromosome with it o F will end up having two copies of the gene interrupted mating is when you stop mating at different points in order to see the phenotypes which can be used to see the order of transformation 0 use this information to make a genetic map of the bacterial plasmid transduction is the exchange of genetic information through page and virus particles 0 also proved with the Davis Utube genes moved through the filter in one direction phage has three parts a head a tail and tail fibers 0 head protein coat and holds DNA inside o tail DNA get injected through the tail to the fibers 0 tail fibers connect to the cell membrane and inject DNA inside lytic lifestyle is the quicker lifestyle for a phage 0 DNA that has been infected with phage DNA replicates codes and produces more phages eventually the cell membrane bursts and the phages are released lysogenic lifestyle is the slower lifestyle for a phage o the DNA is inserted into the bacterial chromosome but stays silent after many replications it enters the lytic lifestyle and becomes active generalized transduction is the mispackaging of bacterial host DNA into the phage head 0 some bacterial genes make their way into the phage and allow recombination to start 0 any gene can be transferred specialized transduction is the inaccurate excision which carries bacterial host DNA along with viral DNA 0 bad for the virus because it is missing part of its genome 0 only a few genes are transferred can map phage chromosomes by assaying for recombinants and by looking at the appearance of the plaque 0 small versus large and clear versus cloudy Benzer did this for r locus using nutritional mutants evaluated them after each generation through complementation tests allowed it to produce proteins but not have time to recombine 0 found that the HI region has 2 cistrons is on two genes deletion mapping is a way to rapidly localize each new mutation o recombinants can t be produced if the deletion strain lacks region with the new mutant Benzers accomplishments o deletion is a mutation point mutations deletion mapping linearity of a gene complementation basis internal structure of a gene mutation hotspots episomes are plasmids that are capable of free replication and able to integrate into bacterial chromosomes horizontal gene transfer is the transfer of genes from one organism to another by a mechanism other than reproduction virus is a simple replicating structure made up of a nucleic acid surrounded by a protein coat 0 can use DNA or RNA single or double stranded round or linear retroviruses are able to integrate into the host genome with help of integrase OOOOOO oncogenes stimulate cell division and cause tumors Chapter 10 Griffith s experiment 0 used 2 types of pneumococcus I rough no polysaccharide coat I smooth virulent R gave no disease 8 gave disease heat killed 8 gave no disease heat killed 8 plus R gave disease conclusion chemical substance of one cell is capable of genetically transforming another cell Avery Macleod McCarty experiment 0 heat killed cells and striped away lipids and carbohydrates kept proteins and nucleic acid DNA and RNA 0 added enzymes that would degrade all three in separate vials 0 added R cells and tested to see if 8 cells appeared had in both protein and RNA vials o conclusion transformation cannot occur unless DNA is present must hold genetic information Hershey and Chase experiment 0 tagged protein with 835 and DNA with P32 of phage 0 let them interact and undergo transduction 0 found only P32 inside of bacterial cells and 835 outside 0 conclusion phage genome is made up of DNA nucleotides are made of a phosphate sugar and base learn structure bases split into two categories 0 purines double rings adenine and guanine o pyrimidine single ring cytosine thymine DNA uracil RNA Watson and Crick 0 used Chargaff39s base ratios Xray crystallography and models found A binds to T with 2 H bonds C binds to G with 3 H bonds strands go in opposite directions major and minor grooves 3 helical forms I A DNA is righthanded less water shorter and wider bases tilted away I B DNA is right handed lots of water most stable I Z is left handed backbone zigzags occurs with many C and G alternating nucleotides RNA has the same backbone as DNA but the 2 OH group makes it more unstable Sanger DNA Sequencing 0 used dideoxy terminates stop replication at certain bases 00000 00000 0 runs replication many times with dideoxy terminators of all bases 0 run through gel electrophoresis measure length read from bottom up 5 to 3 o fluorescent ddNTP is easier than using a radioactive tag 0 dies each terminator a different color reaction in one lane in gel and use laser to see primary structure is nucleotides secondary structure is the stable 3D configuration tertiary structure is the complex packaging arrangement in chromosomes phosphodiester linkages are strong covalent bonds that connect 2 nucleotides in a polynucleotide strand 0 the negative charge of the phosphate group is neutralized by the association of positively charged proteins and metals 0 DNA methylation is when methyl groups are added to bases impacts gene expression and 3D structure Chapter 11 0 simple organisms have small genomes o phage has 5000 bp 0 bacteria has 46 Mbp o eukaryotes have 13Mbp 0 model eukaryotes to memorize o nematodewall cress 100Mbp 0 fruit fly 165 Mbp 0 human 34 Gbp o genome size usually correlates to organismal complexity with variation in size explained by the probability of fixation of mildly deleterious junk DNA variation in genome size is largely due to accumulation of repetitive DNA denaturation is the melting of two strands of DNA apart with heat renaturation is the rehybridization of the two strands done through slow cooling process 0 depends on concentration high is slow low is fast 0 simple sequences renature quicker because any collision between first sequences will result in a match Tm is the melting temp at which half the DNA is melted MarmurDoty Equation 0 W 414 fraction of GC 166 log Na 815 o CCo 1 1 KCot o C is concentration of single strand DNA 0 Co is initial concentration 0 k is a constant determined by experimental conditions 0 CoT Curves o cot on X and fraction reassociated on Y 0 right half of an upside down U 0 move to right as they get less repetitive 0 single copy runs over all of them positive supercoiling is when the DNA is over rotated helix twists on itself negative supercoiling is when DNA is under rotated helix twists on itself in opposite direction DNA together with histones creates nucleosomes which fold up to produce 30nm fibers which then create 300 nm loops which are further compressed to make chromatid histones are the most abundant protein in chromatins small positively charged chromatosome consists of a nucleosome plus the H1 histone nuclease will cut apart individual beads of nucleosomes 200 bp long at the linker DNA segments centromeres are crucial for proper segregation o centromeric repeats tell proteins to bind to allow sites for spindle fiber attachments telomeric repeats at the ends of every chromosome 0 carry own template and are repeated by telomerase 0 protect in order to stop degradation and ends joining to other chromosomes tloop structure ties a degradationresistant knot on the end of chromosome mitochondria and chloroplasts have their own DNA 0 endosymbiosis antibiotics can target translation 0 many targeted at eubacteria o prokaryotic targets can impact mitochondrial translation many genes transferred to nucleus clonal inheritance o organelle DNA inherited uni parentally o mitochondrial and chloroplast DNA is inherited maternally 0 plant mitochondrial DNA is inherited paternally haploid inheritance 0 many mtDNA per mitochondrion hundreds per cell 0 thousands of mtDNA per cell heteroplasmy 0 even though it is haploid copies are not all the same within a cell 0 short molecules may increase in frequency random segregation may result in some with low mitochondrial function mtDNA can cause human disease because of reduced oxidative phosphorylation which leads to dysfunction of energy intensive tissues 0 mutations can relate to aging o segregation of heteroplasmic defects can cause progressive disease euchromatin are chromosomes that undergo the normal process of condensation and decondensation in the cell cycle heterochromatin remain in a highly condensed state throughout the cell cycle including interphase centromere is a constricted region of chromosome where spindle fibers attach half of the human genome is repetitive DNA highly repetitive DNA is short lt1OO bp present in millions of copies that are repeated in tandem and clustered together 0 homoplasmy is when all organelles are genetically identical Chapter 12 0 genetic material carries mutates replicates and expresses genetic information o Meselson and Stahl experiment 0 used cesium chloride density gradient centrifugation machine replicated with heavy and light nitrogen conservative model expected I 1G and ZG one band at heavy and one band at light semiconservative model expected I 16 one band in between light and heavy I ZG one band in between light and heavy one band at light dispersive model expected I 16 one band in between light and heavy I ZG one band closer to light conclusion semiconservative model conservative whole new DNA is made semiconservative one strand is old and one strand is new dispersive DNA breaks up replicates and recombines randomly DNA replication requirements template of single stranded DNA deoxyribonucleotide triphosphates dNTPs DNA polymerase enzyme short oligonucleotide primer free 3 OH group to extend o replication origin is where replication starts 0 O O O initiator proteins bind to origin and unwinds a short stretch allows helicase to attach and move in 5 to 3 direction kept apart by singlestrandbinding proteins breaks H bonds between bases moves replication fork DNA gyrase relieves strain ahead of replication fork through topoisomerase activity RNA polymerase lays primers DNA polymerase III does most of the replicating o bacterial polymerase O poly II can move fonNard and backwards 3 5 exonuclease activity to remove mistakes stuck at primers poly I can get rid of RNA bases and lay down DNA through 5 3 exonuclease activity DNA ligase closes gap where the primer was replisome is a replication machine moving all the enzymes includes sliding clamp Theta Model of Replication E Coli 0 one origin bidirectional 2 replication forks at each end of replication bubble 0 forms a replication bubble ends when the two meet 0 creates 2 connected circles separate 0 Rolling Circle Model of Replication o viruses and plasmids 0 only do the leading strand cleaved at origin undergoes another replication to make second strand 0 multiple circular chromosomes 0 replication is very error prone most can be detected by 3 5 exonuclease activity 0 primary error rates are around 3400 per replication in humans 0 many antibiotics inhibit replication bind to DNA 0 can also break strands and inhibit DNA gyrase o Holliday Junction 0 homologous chromosomes align and there are single strand breaks in the same position free ends migrate to the other DNA strand I this is the holliday Junction branch migration as two strands exchange positions can cut in vertical or horizontal plane I V crossover recombinants I H noncrossover recombinants 0 Double Strand Break Model 0 double strand break in one molecule 0 3 strand invades other helix starts replication and displaces original strand 0 2 Holliday junctions 0 same result with H and V cuts replicons are individual units of replication replication licensing factor attaches to the origin and ensure that each replication takes place only once at each origin removed after 0 polymerase stays in one spot and the DNA is pulled through it Chapter 13 0 primary RNA is a string of nucleotides 0 secondary structure is stable complementary parts match and create a stem and often a loop hairpin structure transcription is the process of creating RNA from a DNA template steps of transcription include o initiation of RNA synthesis no primer needed 0 adding to the 3 end 0 DNA unwinds at the front of bubble and rewinds after 0 consensus sequence is the most commonly encountered nucleotides at this part of the DNA 0 E Coli consensus sequences o 35 is TTGACA 10 is TATAAT upstream from start site but including in promoter holoenzyme is a core RNA polymerase and a sigma factor 0 binds to template once combined with the sigma factor and unwinds o sigma factor is released and RNA poly moved beyond promoter and starts transcription elongation is after the sigma factor is released 0 transcription bubble of around 18 bp 0 RNA is synthesized around 40 nucleotides per second slower than DNA replication which is 2000 per second 0 highly parallel process many transcribing at once tree diagram 0 middle line is DNA 3 on left and 5 on right 0 each branch is RNA with 5 furthest from center RNA poly at point where they touch the trunk o shortest branch is start of transcription rhoindependent termination is when the RNA forms a hairpin structure at the end followed by AU string weak anchor 0 RNA poly pauses because it gets clogged falls off rhodependent termination is when there is a hairpin but no AU string 0 rho protein attaches at chasses RNA poly hairpin allows it to catch up uses helicase activity to separate eukaryotic transcription has more genes and more types of RNA being made RNA Polymerases o poly l makes large RNA 0 poly ll makes premRNA some snRNA snoRNA o poly lll makes tRNA small RNA 0 poly lV makes some siRNA in plants polymerase II creates a right hand turn 90 degrees to open helix 0 DNA enters downstream and exists upstream DNA 0 nucleotides diffuse in collect and held in by amino acid flap 0 RNA exists before DNA core promoter has more enzymes because it is harder to find genes in a bigger genome o TATA box around 25 o TFllD recognition element at 35 o downstream core promoter element at 30 0 positive and negative regulations TBP and TllD find the TATA box other transcription factors bind upstream and all allows major polymerase to bind 0 extra additional upstream enhancer sequences DNase footprinting tells you where the proteins bind the DNA 0 add low concentration of DNase I break at every point gel electrophoresis 0 look at gaps where protein was 0 RNA poly ll transcribes well past coding sequence RAT attaches and chews up with helicase activity to disconnect o ribozymes are catalytic RNA molecules that can cut their own sequences connect to other molecules replicate others and from peptide bonds between amino acids 0 transcription unit is a stretch of DNA that encodes a RNA molecule and sequences for transcription 0 RNAcoding region is a sequence of DNA that nucleotides that is copied into an RNA molecule the transcription apparatus moves downstream first nucleotide transcribed is 1 downstream is positive and upstream are negative abortive initiation is when RNA polymerase generates and releases short transcripts while still bound to promoter happens in both prokaryotes and eukaryotes Chapter 14 o 4 major types of RNA messenger transfer ribosomal various small 0 structure of prokaryotic mRNA looking from 5 on left to 3 on right 0 untranslated region shinedalgarno sequence start codon protein coding area stop codon untranslated region 0 eukaryotic mRNA undergoes processing before turning into protein 0 capping of 5 end polyadenylation of 3 end splicing of introns o 5 cap is created by adding methylguanine to 5 end 0 added backwards o methylation onto base or ribose 0 proteins then recognize and stabilize polyA tail is added to end to help stabilize central dogma helped us to think that the number of nucleotides in a gene was proportional to the number of amino acids 0 later found not true because eukaryotic genes are discontinuous parts not used c eukaryotic coding regions called exons are interrupted by introns all is transcribed and introns are then removed 0 intron splicing starts when the spliceosomes assemble and are mediated by snRNPS 0 U1 attaches to 5 end and U2 attaches to branch point 0 U1 connects to U2 rest is disconnected as a lariat o GTAG rule start and end of intron 0 alternative splicing is when there are multiple cleavage sites can produce different mRNA from single premRNA 0 two types of self splicing introns 0 type 1 requires GTP secondary structure helps to bind protists fungi phage 0 type 2 resembles normal splicing secondary structure some mitochondrial DNA 0 guide RNA s help edit mRNA sequence parts loop out and other nucleotides are inserted to match guide RNA wobble pairing substitution editing is when nucleotides are removed and new are added tRNA has 4 arms and a small stub 0 top is acceptor arm with CCA codon at top o opposite arm has anticodon that is 3 bases and interacts with mRNA codons o uracil but also has other modified bases rRNA is split into a large and small subunit that aren t additive o eukaryotic 608 and 408 but is an 808 overall 0 can undergo methylation be cleaved into intermediates and trimmed to create mature RNA RNA interference is with small RNA silencing complex that gives protein specificity o enzymes to break up double stranded RNA and proteins to target microRNAs produce double stranded regions through hairpins and are incorporated into proteins 0 can bind to inhibit or start degradation collinear means that there is a direct proportion between nucleotide sequence and amino acid sequence RNA remains in the nucleus until it is spliced then it enters the cytoplasm Chapter 15 need at least 3 bases for a codon because that would create 64 different amino acid possibilities only 20 codons random heterogenesis is when there is a predicted ratio for two bases ex G and U not correct ordered triplets use a binding triplet assay 0 tag one tRNA and put down a ribosome and a triplet place over filter 0 radioactivity should be on top of filter if it matches the codon wobble pairing shows that bases don t need to line up perfectly 0 allows for less tRNA need at least 32 genetic code has structure that minimizes mutation effects 0 3rd position is synonymous some 1st positions amino acids vary in R group and in size 0 polar uncharged aromatic positively charged negatively charged R group types 0 similar types are around each other in table there are exceptions to the encoded amino acid that have occurred through evolution 0 don t change a lot of protein codes translation process 0 aa attaches to 3 end of specific RNA I called charging attaches to 3 OH o tRNA synthetase 37 total per cell I enzyme to make sure the right aa pairs with the right tRNA I each can recognize around 3 tRNAs to be more efficient I 20 in nucleus and extra 17 in mitochondria initiation starts when ribosomal subunits are disconnected o 16S rRNA finds shinedalgarno sequence 0 initiation factor F3 binds to small subunit splits up attaches to RNA 0 fMET and tRNA initiation factors bind and release lF3 top ribosome attaches o binds to 5 cap in eukaryotes and slides along until it reaches kozak consensus sequences polyA tail tells it when to stop doesn t waste energy 3 sites in ribosome right to left 0 A adding site 0 P peptidyl site 0 E exit site elongation o fMET and tRNA occupy P site with help from elongation factor next tRNA attaches to A site 0 peptide bond forms between amino acids translocation is a part of elongation o ribosome moves 3 bases down tRNA that was in A site moves to P P moves to E and leaves 0 new tRNA joins A site termination 0 stop codon no tRNA joins c release factor comes in and forms a complex with RF3 and GDP polypeptide released and ribosome released after prokaryotes are able to couple transcription and translocation because they don t have a nuclear membrane antibiotics can disrupt prokaryotic translation by 0 binding to A site binding to ribosomal protein blocking binding oftRNA to A site
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