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88 Cards in this Set
- Front
- Back
How many chromosomes in somatic, diploid cells?
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46 chromosomes (2 each of numbers 1-22 + 2 sex chromosomes)
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Females vs. males chromosomes
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Females have 2X's
Males have X and Y - One from dad and one from mom |
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Compare cells in the body/ makeup of DNA and expression of genes
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- Every single cell in the body has same cell material/ DNA
- Expression of genes changes |
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Size of DNA
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48-280 million basepairs
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What phase is DNA replicated
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S phase
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When do daughter sister chromatides become attached to each other?
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G2, M phase
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Centromere
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joining site, site of microtubule attachement during movement of sister chromatids to opposite m=poles o=in mitoses and meioses
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What is centromeric DNA composed of?
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AT-rich, short (171 bp) satellite repeats
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What is a telomere
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- ends that protect DNAs from shortening during replication
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Number of genes in humans vs. mouse
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27,000-mouse
29,000-human |
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Transposon
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piece of DNA that can jump from one position to another
- create antibiotic resistance in bacteria |
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What percentage is the protein coding region?
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1.5%
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Breakdown- genes, transposons, misc
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Genes- 30%
Transposons- 45% Misc- 25% |
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What is included in breakdown of transposons?
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- 21% LINEs
- 13% SINEs - 8% retrovirus like |
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What is a gene?
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- entire DNA sequence required for synthesis of useful RNA (rRNA, tRNA, mRNA or other RNA)
- includes promoters, enhancers, UTR's |
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What amount is expressable sequences?
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29%
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The protein-encoding, reading frames (without introns) are what percent of genome?
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1.4%-
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What is the rest of DNA that is not expressable sequence or protein encoding?
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Spacer DNA between genes, and half of the spacer DNA is derived from ancient mobile genetic elements, some of which is still jumping form place to place in the genome
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Introns + Exons in Ovalbumin gene and hemoglobin B subunit
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Ovalbumin- 7 introns, 7 exons
Hemoglobin- 3 exons, 2 introns 90, 131, 222, 851, 126 Ex, In, Ex, In, Ex |
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4 steps of cell cycle, what is interphase and mitosis?
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S, G2, M, G1
Interphase- G1, G2, S Mitosis= PMAT |
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Cell cycle: what process occurs between S and G2?
- What are cohesins |
replication and cohesion
- Replication occurs from multiple origins of replication; daughter chromatids are linked by cohesins |
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What occurs between G2 and Prophase of mitosis?
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Condensins add for condensation
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What leaves after prophase? What happens during this time?
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Cohesins leave
- Alignment of chromatids |
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What happens in metaphase?
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DNA condensed
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What occurs between metaphase and anaphase?
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separation of sister chromatids
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What occurs between anaphase and G1?
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- Condensins leave
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Trace chromatid --> DNA
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Two chromatids: 10 coils each
One coil: 30 rosettes One rosette: 6 loops One loop: 75,000 bp 30 nm fiber "Beads on a string" form of chromatin DNA |
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Mutation definition
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permanent change in nucleotide sequence
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Point mutation
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permanent change of single nucleotide
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Long term DNA mutation rate
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Stable DNA mutation rate (mutations in gene pool) is 1% / million years
These mutations are basis of evolutionary process |
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Short term evolution rate
- What happens when somatic cell mutates? |
- Mutations in somatic cells are more frequent and cause 20% of premature deaths in western hemisphere
- Most cancers are clones of cells with mutated DNA |
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Protecting somatic cell protects who? Protecting germline cell DNA protects...
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- Somatic protects individual
- Germline protects species (sperm and oocytes) |
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Types of Mutations (6 types)
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mis- replication
depurinations deaminations alkylations pyrimidine dimers other |
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Mis-replication (frequency and cause)
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- 10^-8 frequency
- DNA damage from environmental factors - 1 error every 10 billion letters |
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Depurinations- what is it, how, how many
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- Spontaneous hydrolysis of the beta N-glycosidic bonds
- Heat fluctuations in nucleus - 5000 / cell/ DAY |
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How do deaminations occur? How many?
What are the products? C, A, G deaminate to what products? |
- Spontaneously
- 100 / cell/ DAY - Unnatural base is product C --> Uracile A--> HX hypoxanthine G --> X (xanthine) |
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Alkylations include what type of mutations? What is the effect?
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- Methylations (metal group attaches)
- Large adducts such as benzo(a)pyrene from smoke - Distort DNA |
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Pyrimidine dimers- what happens? How?
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- UV induced covalent bonds between adjacent pyrimidines on same strand
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Other types of mutations
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- Ring opening
- Oxidation - Cross-linkage - Single and double strand breaks |
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Point Mutations (3)
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Transitions
Transversions Single base insertions/ deletions |
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A. Transitions, give example
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Purine converted to different purine
A--> G Pyrimidine converted to different pyrimidine C--> T |
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With transition mutations, what happens after a round of replication to the base pairs?
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- A-T becomes G-C
- C-G becomes T-A |
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B. Transversions, give example
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Purine converted to pyrimidine
Pyrimidine converted to purine A-C, A-T, G-C, G-T |
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When transitions or transversions occur in gene-encoding a protein, what are 3 possible consequences?
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Neutral- no change in AA
Missense- substitution change of one amino acid Nonsense- creation of a stop codon leading to truncation of the AA sequence |
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Single Base Insertions/ Deletions: causes, consequences
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- Caused by DNA polymerase stuttering
- If in protein reading frame, results in codon frameshift- all downstream codons incorrect - Accidental stop codon crops up in new aberrant reading frame |
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DNA Replication- what is it?
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- Make or reproduce an exact copy
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Eukaryote- length of DNA
- Drosophila - Human |
Drosophila kB = 165, 000
length = 56,000 Human kB = 2,900,000 Length = 990,000 |
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How many origins of replication do stem cells have?
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20,000 origins of replication
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Complexity of DNA- packaging
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All eukaryotic DNAs are folded and packaged into dense, compact structures
- Associated with chromatin |
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What is chromatin?
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tightly packed DNA-binding proteins which help to organize the package
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What is relationship between complexity and replication?
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- Complex structures are impediments to the replication mechanism that requires that two parental strands be totally separated by the end of the process
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What is the meaning of DNA replicated semi-conservatively?
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- Each daughter molecule ends up with a parental strand and a nascent strand
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How is replication semi-discontinuous?
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One strand is replicated continuously from 5'--> 3'
One strand replicates on 3'--> 5' strand, but discountinuously in segments |
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So 2 characteristics of DNA synthesis
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- Semidiscontinuous
- Semiconservative |
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Where does replication start?
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- Origin of replication, or multiple origins in nuclei
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How is timing of replication of both strands related?
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Growth of each "replicon" is bidirectional with both strands being replicated simultaneously
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What enzyme works in replication?
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Synthesis is carried out by DNA polymerases
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What direction do DNA polymerases synthesize?
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5' to 3' direction
- READ TEMPLATE IN 3' to 5' direction |
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What is proofreading by DNA polymerase?
- What 2 types of polymerases lack proofreading? |
3' to 5' exonuclease activity is called proofreading
- Polymerases alpha and beta are exceptions that lack proofreading |
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What types of polymerase have 5 to 3' exonuclease activity that functions in repair? What other activity are they involved in?
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- Prokaryotic DNA Pol I
- Eukaryotic Pol E (epsilon) - Both involved in PRIMER REMOVAL |
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Why is DNA replication thermodynamically favorable? (4 conditions)...Drive polymerase reaction
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1. dNTPs --> dNMPs + PPi
2. PPi --> 2 Pi (loss of product) 3. Base stacking 4. Hydrogen bond formation (adds energy) |
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What is the first step of the replication mechanism?
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1- Initiation at ori (origin of replication)
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What sequences originate the DNA strand?
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- Tandem array of three 13 bp sequences
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What is the significance of the 4 9bp sequences in the DNA
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Binding sites for DnaA protein
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What proteins promote unwinding at ori?
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dsDNA-binding proteins
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Function of ssDNA-binding proteins
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Keep separated ssDNAs in an extended form
- binds to DNA and prevents strands from meeting |
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Function of helicase
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- Uses ATPs to mechanically invade and separate strands at replication fork
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Function of primase
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- Synthesizes short RNA primers of 3-20 nucleotides in length
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Direction of synthesis, free hydroxide
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Synthesis is in the 5' to 3' direction, giving free 3'-OH for subsequent nucleotide extension
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What is the name of primases in eukaryotes?
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Prokaryotes- primase
Eukaryotes- DNA Pol alpha is RNA-synthesizing primase |
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Why is Pol alpha primase different from other DNA polymerases?
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- With exception of Pol alpha, DNA polymerases cannot initiate a new strand (de novo)
- Only elongate a pre-existing primer |
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Function and kinds of DNA polymerases
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- Elongates primer with deoxynucleotides
- DNA Pol alpha, beta, gamma, delta, epsilon |
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DNA Pol alpha function
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Primes both strands
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DNA Pol beta
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functions in repair fo nuclear DNA
- incorporates one nuc and leaves |
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DNA Pol gamma
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carries out all mitochondrial DNA synthesis
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DNA Pol delta
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replication elongation of both strands (very processive)
- DOES MOST OF WORK! |
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What is processivity?
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Avg number of nucleotides added before the enzyme dissociates from the DNA
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DNA Pol epsilon
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involved in repair of nuclear DNA and probably primer removal, using 5' to 3' exonuclease activity
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Prokaryotic DNA polymerases
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DNA Pol I
DNA Pol II DNA Pol III |
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DNA Pol I
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- repair synthesis and primer removal with 5' to 3' exonuclease activity
- First polymerase to be characterized |
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DNA Pol II
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- participates in repair
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DNA Pol III
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- replication elongation (highly processive)
- Does most of replicative work in bacteria |
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Topoisomerase I
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1- Cleaves one strand of parental DNA beyond forks
2- permits further unwinding of parental DNA 3- reseals (rejoins) the nicked ends |
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Topoisomerase II
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- cleaves both strands
- allows unwinding of overwound Watson-Crick strands - rejoins ends |
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What is the cofactor for Topo II?
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- ATP
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What is a version of Topo II in bacteria?
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Gyrase
- makes a double strand scission - forcibly underwinds DNA - reseals scision |
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What is result of undwerwining strain in gyrase?
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- Relieved by supercoiling
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Is topo I or II more important for bacteria?
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- Topo II is more crucial to the viability of the cell
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