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33 Cards in this Set
- Front
- Back
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How is the DNA double helix separated? |
-Helicase uses ATP to unwind the DNA helix. |
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What does single strand binding protein do? |
-SSB binds the single-stranded regions to prevent reannealing or nuclease digestion of the DNA. |
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How is supercoiling adjusted ahead and behind thereplication fork? |
- In order to add or remove supercoils,the DNA strand must be broken by atopoisomerase. -topoisomerase relieves tension by removing 2 supercoils per turn |
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Topoisomerase 1 |
are enzymes that cut one of the two strands of double-stranded DNA, relax the strand, and reanneal the strand. |
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Topoisomerase 2 |
cut both strands of the DNA helix simultaneously in order to manage DNA tangles and supercoils. They use the hydrolysis of ATP, (unlike Type I topoisomerase). change the linking number of circular DNA by ±2. |
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the dna in cells is negatively supercoiled |
this is necessary for both compacting dna and also makes it easier to unwind for strand separation |
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How are new DNA strands synthesized? |
1) nuc attack on 3' OH from nucleic acid on the alpha P of an incoming deoxy nucleotide triphosphate - progressive process 5'--->3' (growing end) |
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E coli has 5 different DNA polymerases |
(DNApoly I-->DNA poly V) |
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How are new DNA strands synthesized? |
DNA polymerase adds deoxynucleotides to the free 3’OH ofan existing strand. ***DNA poly III is the main polymerase for replication Human polymerases have 12 DNA pol lagging strand synthesis DNA pol Epsilon leading strand synthesis |
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How do we get a free 3ʼ OH on the new strand? |
An enzyme, primase, introduces a short RNA primer that iscomplementary to the template strand. provides 3'OH for extending |
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4611 Chapter 20 slides powerpoint.ppt How are new DNA strands synthesized?! |
4611 Chapter 20 slides powerpoint.ppt Since DNA polymeraseextends DNA in the 5’!3’direction, one strand issynthesized continuously(the leading strand) and theother strand is synthesizedin segments called Okazakifragments (the laggingstrand). 5'-->3' limitation needs RNA primer primase to extend each each lagging strand |
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How are the ends of linear DNAmaintained? |
Telomerase-->Telomere |
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What happens if DNA polymerase adds anincorrect base? |
Most DNA polymerases havea proofreading function: thepolymerase slows down dueto the bulge caused by themispairing and a 3’!5’exonuclease removes themisincorporated nucleotide. error rate without proofreading is around 1 in 10,000 bp misincorporatedwith proofreading = 1 in 1,000,000 with dna repair= 1 in 100,000,000 |
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What happens to the RNA primers during replication? |
A 5’-->3’ exonuclease such as RNase H or DNA pol I removesthe RNA primer from each Okazaki fragment. |
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How is the sugar phosphate backboneconnected between Okazaki fragments? |
DNA ligase forms a phosphodiester bond to join neighboringfragments.phosphodiester bond is high energyseals backbones |
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How is DNA packaged within the cell? |
Linear DNA is negatively supercoiled by wrapping the doublehelix around a core of 8 histones to form a nucleosome. |
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Histone |
fundamental unit of DNA, very positive aa residue charges LYS and ARG bond to sugar phosphate backbone positive supercoil more compact negative supercoil easier to separate |
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How do DNA and histones modificationsaffect DNA expression? |
Methylation of cytosine residues in CpG sequencesinactivates genes. Covalent modification of histones may increase or represstranscription. |
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modification to histones such as acetylation of Lys residues can loosen the DNA histone interaction and essentially promote transcription other covalent modifications |
include phosphorylation (recruiting a protein), methylation and ubiquitation DNA as well as histone modifications are important for EPIGENETIC heritable changes that do not involve underlying DNA sequence changes |
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4611 Chapter 20 slides powerpoint.ppt How is DNA packaged within the cell?! |
euchramatin is lightly packed DNA that is heavily transcribed -Euchromatin has less stain that binds than heterochromatin -beads on a string heterochromatin is much more tightly packed DNA 30nm chromatin |
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4611 Chapter 20 slides powerpoint.ppt What happens if DNA is damaged?! |
4611 Chapter 20 slides powerpoint.ppt DNA is subject to oxidative damage (red arrows),spontaneous hydrolysis (blue arrows), and methylation(green arrows), so the cell must have mechanisms torecognize and repair damaged DNA. |
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-cancer |
simply characterized by uncontrolled cell division…does not arise from a single mutation but from accumulated mutations -multiple diseases with multiple origins -these mutations can be induced in a few ways1. environmental factors: carcinogens, smoke, sun2. genetic predispositions: inherited mutation BRCA1 3. infections: HPV, hep B4: spontaneous mutations |
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Why is sunshine mutagenic? |
UV light promotes pyrimidine dimers (most frequentlybetween thymines). forms covalent bonds --> kink -humans use nucleotide excision repair to fix PYRIMIDINE dimers in contrast to most organisms which specifically seek out and splits these dimers with PHOTOLYASE enzyme |
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How do environmental chemicals such asbenzopyrene cause DNA damage? |
Benzopyrene is oxidized in theliver and then forms an adductwith N2 of guanine. causes G->T transversions transversions: mutation that switches a purine and pyrimidine transitions: purine to purine or pyr to pyr mutation |
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How does methylation lead to mutations? |
Methylation of cytosine residues in CpG sequencesinactivates genes. |
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How is DNA methylation repaired? |
Suicide proteins called alkyltransferases, transfer the methylgroup to a cysteine (permanently inactivating the enzyme). |
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What are other common forms of DNAdamage? |
guanine --> 8-oxoguanine: abasic sites: deamination: |
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guanine --> 8-oxoguanine: |
caused by reactive oxygen species such as peroxides G-->T transversions are introduced |
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abasic sites |
r APsites thousands of bases are hydrolyzed by the ribose sugar each day |
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deamination: |
of cytosine is spontaneous ---> uracil. DNA incorporates thymine residue instead of URacil so that deaminations can be identified before they are propagated |
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How does the cell repair some commonforms of damage? |
Base excision repair: cells havespecific glycosylases that recognizecommon errors, such as T-G pairs oruracil, and remove the incorrect base |
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How does the cell repair some commonforms of damage?! |
Nucleotide excision repair: errorsthat significantly distort the helixare repaired by removing asegment of DNA surrounding thedistortion. |
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How are misincorporated bases repaired?! |
After replication, the mismatch repair system scans the newlysynthesized strand and excises any segments withmisincorporated nucleotides. |
