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Cell Bio Test 2 (Got A+ on the test)

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Biological Sciences
BIOL 3090
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BIOL 3090 Sect 1 2006Study Guide for the 100 Point Exam 2Everything we covered is fair game but I have highlighted in bold and underline those topics that I feel are most importantMost of the questions will come from lecture topicsChapter 4 Nucleic Acids Genetic Code and Macromolecular Synthesis22 RNA versus DNA chemical differencesWhich is more stable DNA or RNAWhy B form versus A form versus Z form DNA Fig 44Ribonucleic acid consists of a nitrogenous base adenine guanine cytosine or uracil ribose sugarhas a 2 OH AND a 3 OH and 13 phosphatesDeoxyribonucleic acid consists of a nitrogenous base adenine guanine cytosine or thymine a 2deoxyribose sugarhas an H on the 2 carbon and an OH on the 3 carbon and 13 phosphatesDNA is more stable than RNA because RNA has 2 OH groups at its 2 and 3 carbons which make is more susceptible to nucleoplilic attack2 OH makes RNA very unstableB form DNA most prevalent form in the cell helix is right handed 10 base pairs per turn base pairs nearly perpendicular to the axis of helx make up chromosomes major and minor grooves bases exposed much more inmajor groove than in minorA form DNADNARNA hybrid helices RNARNA helices base stacking more compressed 11 bpturn base pairs severly tilted and off centerZform DNA made in lab alternating Gs and Cs in the two strands sugar phosphate backbone appears to zigzagaka ZDNA23 How do most proteins bind DNA by bending the DNA at the promoter regionWhat groove is usually involvedMajor GrooveWhat interactions occur between DNA and proteinthey make contact with bases via Hbonds and Van der Waals interactions24 Melting dsDNAWhat is the TmWhat does the GC content of DNA do to Tm Fig 46 The Tmis the melting temperature at which 12 of the DNA is single stranded and 12 of the DNA is double strandedThe more GC base pairs the higher the Tm because each GC base pair has 3 H bonds between it while an AT base pair only has 2 H bondsMore H bonds means more temperature and energy is required to break them25 What is supercoilingWhat causes it in bacteria versus eukaryotes Fig 47supercoilingoccurs when a DNA helix is twisted together very tightly like spinning a rubber band together between your fingers supercoiling is caused by gyrases in bacteria while supercoiling occurs as a result of helicase unwinding a portion of the DNA in Eukaryotestopoisomerases regulate the degree of supercoiling by causing nicksTopo I nicks one strand then resealsTopo II cuts both strands then reseals26 TFRNA is always linearName two examples of RNA with higher order structures Fig 48F RNA can be linear circular singleor double stranded 2 examples of RNA with higher order structures are the hairpin and stemloop27 Kinds of RNA in the cell and their relative abundancetRNA3rRNA95mRNA2snRNAminor28 Fig 419 is a good review of protein translationSEE FIGURE 41929 Aminoacyl tRNA synthetases Figs 421link a specific AA to its cognate tRNAs by a high energy ester bondrequires use of ATPthere are 20 different aminoacyl tRNA synthetaseseach enzyme is specific for only one of the 20 AAscharges or activates the tRNA30 The wobble base position Fig 423 how does this relate to the genetic code being redundant degenerateCodon and anticodon parallel or antiparallelthe wobble base position is the first base in the tRNA anticodon and the third base in the corresponding mRNA codonthis allows a single tRNA to recognize more than one codon in the mRNA but bring in the same AA the codon and anticodon are antiparallel31 Ribosome structure and its components Fig 424one ribosome contains 4 ribosomal RNAs and 83 ribosomal proteins in eukaryotesProkaryotic ribosome consists of a large 50S subunit LSU and a small 30S subunit SSU to form the 70S assembled ribosome eukaryotic ribosome consists of60S LSU and 40S SSU to form the 80S assembled ribosomeLSUeukaryotesrRNAs 28S 58S and 5Sproteins50 large subunit proteins called L1L2L3SSUeukrRNA 18Sproteins 33 small subunit proteins called S1S232 Initiation in eukaryotes eIFs SSU m7G Kozaks AUG LSU ATP and GTP hydrolysis Fig 425eIfs keep LSU and SSU separate prior to translation initiation complex forms at the 5 7methyl guanosine cap and scans the mRNA for Kozaks AUGthe start site ATP used to power the initiation complex after a peptidyl tRNA is in the P site and an aminoacyl tRNA arrives in the Asite GTP used qirh eIF 2 to form the preinitiation complex33 Elongation P site versus A site versus E site and the mechanism of elongation Fig 426Termination Fig 429fMettRNA i met is in the P site aminoacyl tRNA goes to A site peptidyl transferase activity of Large rRNA catalzyes peptide bond formation between the AA in the P site and the AA in the A siteGTP hydrolysis causes the ribosome to have a conformational change allowing the next aminoacyl tRNA to enter the a site and ribosome translocationthe A site now has the tRNA with the AAs attached to it and the tRNA from the P site is now is the E siteTermination occurs when release factorsRF1 or RF2 in bac RF1 in euk enter the A site and mimic tRNAs and RF3GTP can bind to provide the energy to cut the peptidyl tRNA bond by GTP Hydrolysis34 Polyribosomes PABI and recycling of ribosomes Fig 431polyribosomes allow multiple ribosomes to be translating the mRNA at oncePABP1 interacts with eIF4G for efficient use of ribosomescausing them to dissociate
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