Term
| To fulfill its role, the genetic material must meet several critera, what are these 4 criteria? |
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Definition
Information- it must contain info necessary to make entire organism
Transmission: It must be passed from parent to offspring
Replication: It must be copied to be passed from parent to offspring
Variation: must be capave of changes to acccount for phenotypic variation |
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Term
| Pneumococcus experiment with smooth and rough bacteria--- What was it trying to prove? |
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Definition
| There is a transforming agent within E coli, DNA is the genetic material |
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Term
| What happened when you injected mice with live S bacteria ? What was recovered from mouse blood? |
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Definition
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Term
| What happened when injected mice with live R cells? |
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Definition
| Mouse survived, no living bacteria isolated from teh mouse's blood |
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Term
| What happened when you inject mouse with heat killed s bacteria? |
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Definition
| mouse survived, no living bacteria isolated from the mouses blood. |
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Term
| What happened when you injected mouse with live type R + heat killed S cells? |
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Definition
| Mouse died, Type S bacteria recovered form the mouse's blood. |
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Term
| What was the conclusion of Griffiths experiment? |
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Definition
| Something from the dead type S was transforming type R into type S, a process called transformation. |
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Term
| Avery, MacLeod, McCarty experiments with cell extracts from type S cells--- what was the purpose? |
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Definition
| The purpose was to identify the genetic material |
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Term
| What four macromolecules did Avery et al test in their prepared cell extracts from type S cells? |
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Definition
| DNA, RNA, proteins, carbohydrates |
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Term
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Definition
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Term
| Type R cells + Type S DNA extract |
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Definition
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Term
| Type R cells + Type S DNA extract + DNAase |
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Definition
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Term
| Type R Cells + Type S DNA extract + RNAase |
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Definition
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Term
| Type R cells + Type S DNA Extract + Protease |
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Definition
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Term
| conclusion of Avery, Macleod, Mccarty experiment? |
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Definition
| Transforming principle is DNA |
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Term
| Hershey and Chase experiment: what did this provide further evidence for? |
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Definition
| That DNA is the genetic material! |
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Term
| Which radisotope was used to label DNA? Protein? |
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Definition
| P 32 labels DNA, S 35 labels protein |
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Term
| what was the result of Hershey chase in terms of data? |
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Definition
In sample containing 35- s labeled phage, agitation in teh blended romves 80 % of the 35 S from the E coli cells
In the sample containing 32 P labeled phage, agitation in the blender removes only 35 % of the 32 P from the E Coli cells |
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Term
| what do the results of Hershey and Chase experiment suggest? |
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Definition
| suggest that DNA is injected in to the bacterial cytoplasm during infection; this is the expected result if DNA is the genetic material |
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Term
| Gierer and Schramm TMV viruses experiment--- tell me about it |
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Definition
| they isolated RNA from the TMV. purified RNA caused the same lesions as intact TMV viruses; therefore the viral genome is composed of RNA |
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Term
| What are the three components of nucleotides? |
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Definition
| phosphate group, pentose sugar, nitrogenous base |
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Term
| in DNa the sugar is ______________ and the bases are __ ___ ___ and __ |
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Definition
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Term
| in RNA, the sugar is ______ and the bases are ____ |
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Definition
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Term
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Definition
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Term
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Definition
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Term
| nucleotides are covalently linked together by what type of bonds |
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Definition
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Term
| What molecules form the backbone of the nucleic acid strand? |
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Definition
| phosphate and sugar molecules |
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Term
| A phosphate connects the _______ of one nucleotide to the ______ of another to make a strand of directionality ______ |
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Definition
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Term
| Paulings contribution to double helical structure of DNA |
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Definition
| Pauling proposed that regions of protein can fold into a secondary structure- alpha helix |
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Term
| Rosalind Franklns contribution to double helical structure |
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Definition
| franklin used x-ray diffraction to study wet fibers of DNA; the diffraction pattern she obtained suggested several structure features of DNA---- helical, more than one strand, 10 base pairs per complete turn |
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Term
| Chargaff experiment what was the goal |
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Definition
| an analysis of the base composition of DNA in different species may reveal important features of structure in DNA |
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Term
| what type of cells did Chargaff use in his experiment? |
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Definition
| e coli, streptococcus pneumoniae, yeast, turtle red blood cells, salmon sperm cells, chicken red blood cells, human liver cells |
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Term
| What was the compelling observational result of Chargaffs experiment? |
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Definition
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Term
| Watson and Crick, what was their initial early hypothesis that was incorrect, involving Mg ++ |
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Definition
| Sttrands interact through phosphate Mg ++ crosslinks |
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Term
| What are the key features/ general structural features of DNA double helix? |
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Definition
| two strands are twisted together around a common axis, there are 10 bases and 3.4 nm per complete twist, two strands are antiparallel; one runs in the 5' to 3' direction and the otehr 3' to 5', the helix is right-handed, as it spirals away from you , the helix turns in a clockwise direction. |
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Term
| What is the double helical structure stabilized by? |
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Definition
Hydrogen bonding between complementary bases: A is bonded to T, C is bonded to G
Also stabilized by base stacking-- within the DNa the bases are oriented so that hte flattened regions are facing each other |
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Term
| There are two asymmetrical grooves on the outside of the helix, discuss this |
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Definition
| Major and minor groove, certain proteins can bind within these grooves they can thus intereact witha particular sequence of bases |
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Term
| Triplex DNA--- where does the synthetic band strand bind and according to what rules |
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Definition
| the synthetic strand binds to the major groove of the naturally occuring double strand, the pairing rules that T binds to AT pair and C binds to a GC pair in biological DNA |
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Term
| What are some of the results of synthetic DNA binding to a gene |
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Definition
| it inhibits transcription and can even cause mutations that inactivate the genes function, thus synthetic DNA could be used to silence genes |
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Term
| What is typical length of RNA strands |
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Definition
| typically several hundred to several thousand nucleotides in length |
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Term
| What is the secondary structure a result of in RNA molecules |
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Definition
| complementary base pairing of A to U and C to G |
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Term
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Definition
| structures that contain the genetic material, complexes of DNA and proteins |
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Term
| What is the main function of the genetic matierla |
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Definition
| store information required to produce an organism |
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Term
| What are DNA sequences necessary for? |
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Definition
| Synthesis of RNA and cellular proteins, replication of chromosomes, proper segregation of chromosomes, compaction of chromosomes so tehy can fit within living cells |
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Term
| Self assembly usually occurs in viruses with a simple structure? |
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Definition
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Term
| What two main functions do non capsid proteins usually have? |
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Definition
1) carry out the assemly process ( scaffolding proteins that are not part of the mature virus)
2) act as proteases that cleave viral capsid proteins; this yields smaller capsid proteins that assemble correctly |
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Term
| In what region is the bacterial chromosome found? |
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Definition
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Term
| What type of sequences account for the majority of bacterial DNA? |
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Definition
| structural gene sequences ( encoding proteins) |
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Term
| What roles do repetetitve DNA sequences play |
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Definition
| DNA foliding, DNA replication, gene regulation, genetic recombination |
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Term
| To fit within the bacterial cell, the chromosomal DNA must be compacted about ____ fold |
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Definition
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Term
| Different conformations that result from supercoiling are referred to as |
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Definition
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Term
| Chromosomal DNA in bacteria is positively or negatively supercoiled? |
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Definition
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Term
| What are the two major effects of negative supercoiling? |
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Definition
| it helps in the compaction of the chromosome and it creates tension that may be released by DNA strand seperation |
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Term
| The control of supercoiling in bacteria is accomplished by which two main enzymes |
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Definition
| DNA gyrase and DNA topoisomerase |
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Term
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Definition
| also termed DNA topoisomerase II introduces negative supercoils; it can also relax posiitve super coils when they occur |
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Term
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Definition
| relazes negative supercoils |
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Term
| The competing action of which two enzymes governs the overall supercoiling of bacterial DNA? |
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Definition
| DNA gyrase and topoisomerase I |
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Term
| What can you block the functio of to cure bacterial diseases? |
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Definition
| You can block the function of gyrase because its introduction of negative supercoils is crucial for survival of bacteria |
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Term
| what are the two main classe of drugs that inhibit gyrase and other bacterial topoisomerases? |
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Definition
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Term
| Is the variation in size related to the complexity of the species? |
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Definition
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Term
| What is the difference in the size of the genome due to? |
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Definition
| the accumulation of repetitive DNA sequences |
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Term
| Three types of DNA sequences are required for chromosomal replication and segregation....what are these |
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Definition
| origins of replication, centromeres, and telomeres |
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Term
| What functions do telomeres serve? |
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Definition
| serve important functions in the replication and stability of chromosomes. They prevent chromosomal rearrangements such as translocations. They also prevent erosion into gene sequences when chromosomes shorten during DNA replication. |
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Term
| In eukaryotes, chromosomes contain origins of replication about every________ bp |
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Definition
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Term
| Unique or non-repetitive sequences |
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Definition
| found once or a few times in the genome, includes structural genes as well as intergenic areas ) exons, introns and other parts of genes such as enhancers, and unique noncoding DNA), in humans make up roughly 41% of genome |
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Term
| Moderately repetitive sequences |
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Definition
| found a few hundred to a few thousand times, includes genes for r RNA and histones, origins of replication, transposable elements |
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Term
| Highly repetitive sequences |
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Definition
| found tens of thousands to millions of times, each copy is relatively short, a few nucleotides to several hundred in length. some sequences are interspersed throughout the genome example the ALu family in humans. Pther sequences are clustered together in tandem arrays AATAT and AATATAT sequences in Drosophila these are commonly found inthe centromeric regions |
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Term
| A renaturation experiment can provide quantitative information about: |
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Definition
| complexity of DNA sequences |
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Term
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Definition
| the repeating structural unit within eukaryotic chromatin is the nucleosome, composed of double stranded DNA wrapped around an octamerof histone proteins |
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Term
| What are the 5 types of histones? |
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Definition
| H2a, H2B, H3, and H4 are the core histones, H1 is a linker histone it binds to linker DNA and to nucleosomes but not as tightly as the core histones |
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Term
| What are the two parts of a histone protein? |
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Definition
| globular domain and a flexible, charged amino terminus or "tail" |
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Term
| what is the hypothesis of Nolls experiment? |
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Definition
| test the beadson a string model of chromatin structure |
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Term
| What should happen if the bead on a string model is collect in Nolls experiment? |
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Definition
| DNase 1 should cut in the linker region thereby producing DNA pieces that are about 200 bp long |
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Term
| What did Nolls basically do in the experiment? |
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Definition
| Incubate nuclei from rat lier cells with low, medium and high concentrations of Dnaase1, extract the DNA, and visualize the DNA fragments by staining the DNA and fluorescing with UV light |
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Term
| What was the result of Nolls experiment? |
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Definition
| at high DNase cocentration the entire sample of chromosomal DNA was digsted into fragments of appriximately 200 bp in lnegth, the length of DNA containing one nucleosome |
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Term
| the 30 nm fiber shortens the total length of DNA another _____ fold over the basic beads on a string structure |
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Definition
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Term
| What two models have been proposed for the 30 nm fiber? |
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Definition
| solenoid model and three D zigzag model |
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Term
| Which histone plays a role in the compation of the beads on a string to the 30 nm fiber? |
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Definition
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Term
| How are chromosomes further compacted past the 30 nm fiber? |
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Definition
| chromosomes are further compacted by anchoring the 30 m fiber into radial loop domains along the nuclear matrix |
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Term
| Wrapping DNA around histone octamers to form the nucleosome beads on a string structure followed by formation of the 30 nm fiber shorten teh DNA by about ___ fold |
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Definition
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Term
| What is the nuclear matrix composed of |
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Definition
the nuclear lamina,a collection of fibrous proteins that line the inner nuclear membrane
inner nuclear matrix of proteins |
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Term
| MARS and SARS, what are they and where do they bind |
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Definition
| matrix attachment regions and scaffold- attachement regions, contain high percentages of A and T bases, bind to the nuclear matrix and create radial loops |
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Term
| How is the attachment of radial loops to the nuclear matrix important? |
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Definition
1) it plays a role in gene regulation
2) it serves to organize the chromosomes within the nuclues, each chromosome in the nucleus is located in a discrete and non overlapping chromosome territory |
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Term
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Definition
| less condensed regions of chromosomes that are transcriptionally active, these are regions where 30 nm fiber forms radial loop domains |
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Term
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Definition
| tightly compacted regions of chromosomes that are generally transcriptionalyl inactive, in these regions teh radial loop domains are compacted even further |
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Term
| Two types of heterochromatin? |
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Definition
constitutive- regions that are always heterochromatic and pernanently inactive with regardto transcription
facultative regions that can interconvert between euchromatin and heterochromatin ( for exampple the Barr body which is formed in femamle mammamls when one of the two X chromosomes is converted to a heterochromatic state during embryonic development of somatic cells) |
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Term
| Level compaction leading to metaphase chromosome |
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Definition
| DNA double helix---> nuclesomes ---> 30 nm fibers ---> radial loop domains---> further compaction of radial loops--> formation of scaffold from the nuclear matrix and further compaction of all radial loops ---. the metaphase chromosome |
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Term
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Definition
| multiprotein complexes that help form and organize metaphase chromosomes, both contain a catefory of proteins called SMC proteins ( structural maintenenance proteins) |
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Term
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Definition
| use energy from ATP and catalyze proteins in chromosome structure, together topoosomerases SMC proteins have been shown to promote major changes in DNA structure |
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Term
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Definition
| plays a critical role in sister chromatid alignment, as M phase begins , condensin coats the individual chromatids as euchromatin is converted to heterochromatin |
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Term
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Definition
| plays a critical role in sister chromatid alignment , after S phase and until the middle of prophase, sister cromatids remain attached to each other along their lengths, By middle to late prophase cohesin located along the arms of chromosome is released allowing the arms to sepearte. At anaphase cohesin molecules that remained at the centromere are degraded by a protease allowing the sister chromatids to seperate |
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Term
| How is replication initiated in bacterial chromosomes? |
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Definition
| binding of DnaA proteins to the five DnaA box sequences, this binding stimulates the cooperative binding of additional DnaA proteins to form a large complex |
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Term
| Three types of DNA sequencess in oriC are functionally significant |
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Definition
| AT rich region, DnaA boxes, GATC methylation sites |
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Term
| AFter DNA replication is initiated what happens with AT-rich region etc |
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Definition
| proteins that cause DNA to bend also bind, this causes teh region to wrap around the DnaA proteins and sepearte the AT - rich region, THe DnaA proteins, assisted by the DnaC protein, recruit DNA helicase enzymes ( DnaB protein) to this site |
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Term
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Definition
DNA helicase encounters a double stranded region, it breaks the H bonds between the two strands, thereby generating two strnds
two DNA helicase begin strand sepearation within the oriC region and continue to separate the DNA strands beyond the origin
the DNA helicases separate the DNA in both directions creating two rep for,s outward from oriC in opposite directions, this initiates rep of the bacteria chromosome in both directions an event termed bi directional replication |
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Term
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Definition
| travels ahead of the helicase and alleviates positive supercoiling |
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Term
| SIngle stranded binding proteins |
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Definition
| bind to the sepearted DNA strands to keep them apart |
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Term
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Definition
| synthesize short 10-12 nucleotide RNA primers |
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Term
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Definition
| responsible for synthesizing the DNA of leading and lagging strands |
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Term
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Definition
| excises RNA primers and fills in with DNA |
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Term
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Definition
| covalently links the okazaki gragments |
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Term
| DNA polymerase II has ho wmany subunits? |
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Definition
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Term
| Polymerase I has how many subunits |
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Definition
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Term
| characteristics of catalytics subunit of bacterial DNA polymerasses |
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Definition
| structure resembles a human hand, template DNA threads through the palm, thumb and fingers aroundt he DNA, incoming dNTPs enter the catalyics site, bind to the template strand according to teh AT/GC rule , and then are covalently attached to the 3' end of the growing strand |
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Term
| DNA polymerases can or cannot intiate DNA synthesis |
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Definition
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Term
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Definition
One RNA primer is made at the origin
DNA polymerase III attaches nucleotides continuously in a 5' to 3' direction as it slides toward the opening of the replication fork |
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Term
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Definition
synthesis is also in the 5' to the 3' direction, however it occurs discontinuously away from the replication fork,
Many RNA primers are required; DNA polymerase III uses the rNA primers to synthsize small DNA fragments (1000 to 200 nucleotides each) that are termed Okazaki fragments after their discoverer
DNA polymerase I removes the RNA primers and fills the resulting gap with DNA, it uses 5' to 3' exonuclease activity to digest the RNA and its 5' to 3' polymerase activity to replace with DNA
AFter the gap is filled a covalent bond is still missing; DNA ligase catalyzes a phosphodiester bond thereby connecting DNA frags |
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