Term
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Definition
| the process by which a DNA molecule is copied |
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Term
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Definition
| a change in genotype and phenotype due the assimilation of external DNA by a cell |
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Term
| Describe Griffith's experiment and it's implications |
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Definition
| Studied two strains of the bacterium in mice, one of which was lethal and one of which was benign. he took a portion of the the lethal strain and heated it until it died. he then proceeded to inject a sample of the heat killed bacterium into a mouse and compare it with the effects of a mouse injected with a mixture of the heat killed cells mixed with living benign cells. He found that the mouse injected with only the heat killed cells survived while the mouse injected with the mixture of heat and living benign cells perished and the pathogenicity of the original mixture was passed on to further generations of bacterium. this lead to griffith coining the term transformation and the idea of a change in a genotype and phenotype due to the assimilation of external DNA by a cell. |
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Term
| Describe Avery's efforts to identify the transforming substance |
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Definition
| Avery guessed that DNA, RNA, or proteins were responsible for genetic transformation. He broke open the heat-killed pathogenic bacteria and proceeded to extract samples of DNA, RNA, and proteins. he then proceeded to treat each sample with a deactivating agent and then compare the abilities of each cellular component when activated and deactivated to transform live nonpathogenic bacteria. only DNA was able cause transformation, leading to Avery's conclusion that DNA was responsible for the transfer of genetic material |
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Term
| bacteriophages, aka phages |
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Definition
| viruses that infect bacteria |
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Term
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Definition
| an entity that is essentially DNA enclosed by a protective protein coat. to reproduce, they most infect a cell and take over the cell's meatbolic machinery |
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Term
| Describe the Hershey-Chase example and its implications |
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Definition
| Hersey and Chase set out to prove that protein was responsible for the transfer of genetic material rather than DNA. They used radioactive isotopes of sulfur to tag the protein (attaches to disulfide bridges) of one batch of T2 phages and phosphorus (to attach to the phosphate-sugar backbone) to tag DNA. they then used each batch separately infect E. coli bacteria. Upon examining the E. coli, they observed traces of radioactive phosphorus which implied that genetic material is passed by DNA rather than proteins. |
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Term
| What three elements does DNA consist of? |
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Definition
DNA is a polymer of nucleotides, and is composed of:
1. deoxyribose (a pentose sugar)
2. a nitrogenous base (either A,T,C, or G)
3. and a phosphate group |
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Term
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Definition
1. the base composition varies between species
2. within a species, A=T and G=C |
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Term
| Describe the work of Watson and Crick |
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Definition
| Watson and Crick pulled from the research of Wilkins and Franklin who had been studying protein structure with x-ray crystallography. Watson saw these photos and made the connection that the structure must be helical. the photo also showed that the helix was comprised of two strands and provided Watson with information regarding the helix's width and spacing of the nitrogenous bases. they then used franklin's unpublished report and discovered that the sugar-phosphate backbones were on the outside of the helix. They constructed an antiparallel model double helix model |
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Term
| what are the dimensions of the double helix? |
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Definition
| the double helix makes a full turn every 3.4nm with bases stacked .34nm apart and having 10 base-pairs in every rotation. the diameter of the helix is 2nm |
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Term
| why do the bases only bond with their complements? |
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Definition
| the bases only bond with their complements because it creates a uniform diameter |
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Term
| What bases bond to each other? What are the implications of these specific bonding patterns? |
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Definition
| adenine can form two h-bonds with only thymine, and guanine forms three h-bonds with only cytosine. this supports the first of chargiffins rules |
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Term
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Definition
| the point in the DNA at which replication begins; characterized by a particular sequence of nucleotides (the ORI sequence) containing a large number of A-T bonds |
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Term
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Definition
| single strand DNA; in DNA replication, the DNA after it is separated to serve as the template for replication |
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Term
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Definition
| double-stranded DNA; two DNA strands with complemntary base-pair sequences joined by hydrogen bonds |
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Term
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Definition
| point at which the two DNA strands begin to separate for replication |
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Term
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Definition
| gap in the DNA formed as the replication fork expands |
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Term
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Definition
| enzyme that binds to the ORI sequence and unwinds the dsDNA at replication forks |
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Term
| single-strand binding proteins (SSB) |
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Definition
| proteins that bind to and stabilized the ssDNA after helicase unwinds it |
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Term
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Definition
| enzyme that builds an RNA primer to being DNA replication; one primer is used for the leading strand, and several primers are used on the lagging strand to create Okazaki fragments |
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Term
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Definition
| enzyme that prevents the double helix from becoming "overwound" during DNA replication by breaking one strandm turning it, and then rejoining it |
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Term
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Definition
| enzymes that synthesize new DNA strands in the 5' to 3' direction using the parental DNA as a template; in DNA replication, DNA polymerase III adds nucleotides to the 3' end of the RNA primer, and DNA polymerase I removes the RNA primer and replaces it with DNA |
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Term
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Definition
| joins together fragments of DNA; in DNA replication, joins the newly replaced primer DNA to the leading strand and joins the Okazaki fragments together on the lagging strand |
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Term
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Definition
| binds DNA polymerase III to the DNA, preventing the polymerase from detaching |
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Term
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Definition
| newly formed ssDNA complementary to the parental DNA, synthesized continuously towards the replication fork as it expands |
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Term
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Definition
| complementary ssDNA synthesized with polymerase moving away from the replication fork; synthesized in several small segments called Okazaki fragments |
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Term
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Definition
| a small segment of DNA formed on the lagging strand using an RNA primer |
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Term
| types of bonds present in DNA |
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Definition
A-T have 2 hydrogen bonds
C-G have 3 hydrogen bonds |
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Term
| Why do ORI sequences have many A-T bonds? |
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Definition
| ORI sequences have a multitude of A-T bonds because the 2 H-bonds found here are easier to break than the 3 H-bonds of C-G |
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Term
| Messelson-Stahl experiments |
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Definition
| labeled the nucleotides of the old strands with a heavy isotope of nitrogen, while any new nucleotides were labeled with a lighter isotope. the first replication produced a band of hybrid DNA, which eliminated the conservative model. a second replication produced both light and hybrid DNA, eliminating the dispersive model and ultimately supporting the semi-conservative model |
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Term
| Prokaryotic vs. Eukaryotic replication |
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Definition
Prokaryotic replication:
1. only has one ORI
2. circular chromosome
3. replication bubble expands in both directions until 2 daughter DNA strands are created
eukaryotic:
1. multiple ORA sequences and replication bubbles
2. the multiple rep. bubbles expand and evenutually join into 2 daughter strands of DNA |
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Term
| conservative model of replication |
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Definition
| parental strands come back together after replication |
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Term
| semi-conservative model of replication |
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Definition
| parental strand ends up paired with one of the daughter strands. supported by watson and crick's model |
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Term
| dispersive model of replication |
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Definition
| sections of the parental strand end up integrated and paired with the daughter strands |
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Term
| where can DNA polymerases add nucleotides? |
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Definition
| DNA polymerases can only add nucleotides to the 3' end |
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Term
| why is primase a necessary in replication? |
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Definition
| primase is necessary in replication because it creates a RNA primer with a 3' end, which allows for a new DNA strand to be made |
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Term
| what direction does a new strand of DNA elongate in? |
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Definition
| new DNA strands only elongate in the 5' to 3' direction. |
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Term
| what is the consequence of anti-parallel structure in replication |
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Definition
| the anti-parallel structure requires that lagging strands use Okazaki fragments to be created by the attachment and detachment of DNA polymerase with synthesis back towards previous fragments. this allows DNA ligase to remove the RNA primers between segments and join the 3' of the just synthesized fragment to join with the 5' end of the previous strand where the RNA primer used to be. |
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Term
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Definition
| helps to replace the RNA primer with nucleotides for DNA, but does not join the fragments |
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Term
| what direction does the leading strand move in? |
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Definition
| the leading strand continuously moves and in the 3'-->5' direction synthesizing a 5'-->3' daughter strand |
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Term
| what direction does the lagging strand move in? |
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Definition
| the lagging strand cannot synthesize moving in the 5'-->3' direction, so it uses DNA polymerase to build Okazari fragments to 'hop' down the bubble and synthesize moving in the 3'-->5' direction back toward the ORI and join multiple 5'-->3' fragments that |
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Term
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Definition
| repair enzymes correct errors in base pairing |
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Term
| nucleotide excision repair |
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Definition
| nuclease cuts out and replaces damaged stretches of DNA |
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Term
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Definition
| cuts out and repairs damaged stretches of DNA in nucleotide excision repair |
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Term
| what protein is involved in enlongation? |
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Definition
| DNA polymerases add nucleotides only to the free 3' end of a growing strand, therefore a new DNA strand can only elongate in the 5'-->3' direction |
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Term
| what problem appears to rise from the fact that a DNA polymerase can add nucleotides only to the 3' end of a preexisting polynucleotide? |
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Definition
| this would mean that the usual replication machinery would provide no way to complete the 5' ends of daughter strands, and as a result repeated rounds of replication would produce shorter and shorter DNA with uneven/staggered ends. but this problem would only be applicable to eukaryotes because prokaryotes have circular chromosomes |
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Term
| how is the the potential problem of DNA shortening and uneven ends avoided? |
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Definition
| nucleotide sequences with telomers at their ends containing repetitions of one nucleotide sequence. this acts as a kind of buffer, posponing the erosion of genes located near the end of DNA molecules |
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Term
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Definition
| ends of nucleotide sequences that are repetitive of short nucleotide sequences. provide protection to the ends of DNA. often shorter in older cells |
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Term
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Definition
| an enzyme that catalyzes the lengthening of telomers in eukarotic germ cells, thus restoring their original length and compensating for the shortening that occurs during DNA replication |
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Term
| what type of charge does the backbone of the double helix create? |
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Definition
| the phosphate groups along the backbone contribute a negative charge along the outside of each strand |
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Term
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Definition
| proteins that are responsible for the first level of DNA packing in chromatin. the total mass of this protein is approximately equal to the mass of DNA. more than a fifth of it's amino acids are positively charged so they can bind with DNA |
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Term
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Definition
| the basic unit of DNA packing, "beads" of unfolded chromatin |
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Term
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Definition
| the histone-DNA complex that fits into the nucleus through a complex packing system in eukaryotic cells |
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Term
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Definition
1. DNA binds with histones to create nucleosmes or "beads on a string" that is 10nm in diameter
2. interactions between the histone tails of one nucleosomes with the linker DNA causes the the 10nm fiber to coil or fold creating a 30nm fiber
3. 30nm folds to create 300nm fiber, eventually forming a chromatid that is 700nm |
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Term
| how do we know the packing process is highly specific and precise? |
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Definition
| particular gens always end up located at the same places in metaphase chromosomes, indicating that the packing steps are highly specific and precise |
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Term
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Definition
| created as a cell prepares for mitosis by the folding and coiling of chromatin |
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Term
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Definition
| a highly condensed statee similar to that seen in a metaphase chromosome |
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Term
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Definition
| "true chromatin" a less compacted and more dispersed form |
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