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90 Cards in this Set
- Front
- Back
Which eukryotic DNA polymerase contains primase and initiates DNA synthesis?
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Pol alpha
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Which eukryotic DNA polymerase functions in repair but has no proofreading ability?
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Pol Beta
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Which eukryotic DNA polymerase replicates mitochondrial DNA?
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Pol Gamma
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Which eukryotic DNA polymerase elongates the leading strand and okazaki fragments?
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pol delta
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Which eukryotic DNA polymerase functions in repair and has proofreading ability?
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Pol Sigma
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______ _______ is RNA directed DNA polymerase that is seen in transposons and some viruses.
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Reverse Transcriptase
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_______ maintains telomeric length in cells.
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Telomerase
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Eukaryotic DNA is associated with tightly bound basic proteins called what?
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Histones
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Histones are positively charged at physiologic pH as a result of their high content of which two amino acids?
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lysine and arginine
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The ________ ends of histones can be acetylated, methylated, or phosphorylated and these modifications serve what purpose?
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N-terminal ends: they influence how tightly the histones bind DNA and thereby affect transcription of genes.
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___ _______ can fuse two pyrimidines (usually thymines) adjacent to each other in the DNA, producing a dimer.
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UV radiation
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This DNA damaging agent can cause double stranded breaks:
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High energy ionizing radiation.
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proteins associated with mismatch repair is associated with which condition?
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Hereditary nonpolyposis colorectal cancer (HNPCC)
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This process allows more than one protein to be made from a single gene:
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alternative splicing
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Many genes occur in ______ representing structually related proteins.
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Families
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This is the largest human gene and links muscle contractile elements to the cell membrane:
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Dystrophin
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What process is responsible for the fact that the proteome is significantly larger than the genome?
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alternative splicing
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Most SNPs are ______ the protein coding regions.
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Outside
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The most common type of polymorphism:
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SNP (Single Nucleotide Polymorphisms)
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_______ is a different form of a particular gene- SNPs contribute to this difference.
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Allele
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This SNP results in a change in amino acid in a protein:
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Nonsynonymous.
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How can SNPs outside the coding region can be associated with phenotypes?
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If they affect the process of gene expression (transcription, splicing, etc.)
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Mitochondrial DNA contains information about some proteins, all other mitochondrial proteins are encoded where?
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In the nuclear genome- they're then translated in the cytoplasm and imported into the mitochondria.
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Several genetic diseases of strict maternal inheritance are caused by mutations in ______ ______.
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Mitochondrial DNA
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Name the three components of nucleotides:
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1. 5 carbon sugar
2. Organic base 3. Phosphate |
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_______ bases contain a 9 atom ring. What are the two types?
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Purines - Adenine and Guanine
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______ bases contain a six atom ring. What are the three types?
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Pyrimidine - Cytosine, uracil and Thymine
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A purine or pyrimidine base linked to a sugar:
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Nucleoside
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The first sugar is linked to a phosphate in a nucleotide by a ________ bond.
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Phosphoester
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The second and third phosphates are linked to the nucleotide by ________ bonds.
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Phosphoanhydride
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Why can a nucleoside enter a cell more easily than a nucleotide?
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Because the phosphate group on the nucleotides is negatively charged and cannot go into and out of cells easily.
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The drug 5-flurouracil is converted to its active form _______ in the body.
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5-FdUMP
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How does 5-FdUMP inihibit tumor cell replication?
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Through inhibition of thymidylate synthase (TS) which is needed for de novo synthesis of pyrmidines (C, T and U)
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Approximately 85% of an intravenous dose of 5-FU is inactivated in the liver by _________.
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Dihydropyrimidine dehydrogenase (DPYD).
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DNA is linked by _______ bonds between which two ends?
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phosphodiester bonds between the 3' and 5' ends of adjoining residues.
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Which base pairs are more themally stable?
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G-C base pairs.
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Each turn of the DNA helix contains on avg. _____ base pairs.
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10.5
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The major form of DNA is called ______.
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B DNA
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Generally, ______ is single stranded nucleic acid.
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RNA
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Unlike DNA, the base pairing in RNA is _________.
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intramolecular
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The temperature at which 50% of DNA is melted.
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Melting temperature (Tm)
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The ________ effect is related to base stacking interactions in double standed DNAm which decreases the absorption of light.
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Hypochomic Effect
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The peak of absorbance of DNA is _______.
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260 nm
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The amount of absorbed light for ______ _______ DNA is about 50% less than that for _________ ________ DNA.
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Double stranded absorbs about 50% less light than single stranded.
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A highly ordered complex of DNA and protein.
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Chromatin
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_______is not part of a core nucleosome but a linker histone associated with the linker region between nucleosomes.
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Histone H1
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The presence of this histone causes the nucleosomes to assmeble into a 30nm fiber.
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Histone H1
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NH2 groups of ______residues in the terminal tails of the core histones can be modified.
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Lysine
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Name two common histone modifications:
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acetylation and methylation
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________ of histones decreases the net positive charge in the region. What is the effect of this?
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Acetylation. DNA is less ithgtly bound to histones, may be accessible to transcription machinery.
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Which two enzymes are associated with histone acetylation?
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Histone Acetyl Transferases (HAT) and Histone deacetylases (HDAC)
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Highly condensed form of chromatin, transcriptionally inactive:
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heterochromatin
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Less condensed form of chromatin, transcriptionally active:
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Euchromatin
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The physcial ends of the chromosome that have highly repetetive DNA sequences and are devoid of genes:
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Telomeres
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This structure in telomeres stabilizes the chromosome by allowing the cell to distinguish it from ends of DNA broken due to damage:
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G-quartet
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Difference in DNA sequence between individuals:
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Polymorphism
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phenotype associated with quantitative loss of function, loss of one allele results in phenotype, production of both alleles needed for normal function.
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Haploinsufficiency
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The proportion of individuals carying a mutant allele that have an associated phenotype:
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penetrance
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Point mutation that does not affect the amino acid sequence of the protein:
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synonymous SNP
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A point mutation that changes one amino acid for another:
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Missense mutation (non-synonymous SNP)
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When an amino acid is changed to one of three termination codons:
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nonsense mutation
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What are the three termination codons?
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UGA, UAA, UAG
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Short, repetetive sequences of 1, 2, or 3 amino acids that can be unstable and undergo expansion that increases the number of repeats:
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Microsatellite sequences (aka VNTR)
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The number of ______ among individuals is highly polymorphic and can be used in DNA fingerprinting:
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VNTR's
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Term for increased severity of symptoms and/or earlier age of onset within subsequent generations in a pedigree.
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Genetic anticipation
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What are the two common retro-transposons in humans?
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Alu and L1
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What is the major human LINE element capable of transposition and possibly of disrupting gene function?
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L1
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What is the major human SINE element that is capable of transposition?
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Alu
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________ recognizes Uracil as a foreign base in DNA and cleaves the glycosidic bond.
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DNA Glycosylase
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Covalently linked cyclobutane pyrimidine dimers (thymine dimers) are caused by what?
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UV light
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Pyrimidine Dimers are repaired by __________.
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Nucleotide Excision Repair (NER)
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These are important detoxifying enzymes in the body that make drugs and other foreign chemicals in the body into more water soluble compounds that can be excreted:
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Cytochrome p450
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This enzyme converts a pro-carcinogen in cigarettes into a carcinogen by generating epoxides and other reactive oxygen species that covalently attach to DNA
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Cytochrome p450
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Recombination of free ends is used to repair what kind of DNA damage?
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Double stranded breaks
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What are the two ways to repair double stranded DNA breaks? Which is more error prone?
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1) Homologous Recombination
2) Non-Homologous End joining Non homologous end joining is more error prone |
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Recognizes DNA that doesn't contain telomeres and realigns them:
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Non-Homologous End Joining (NHEJ)
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How is the parent strand identified for DNA mismatch repair?
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Because DNA is methylated at specific sites (hemi-methylation)
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In DNA mismatch repair, the hemi-methylated site is recognized by the protein _____ and the mismatched base is recognized by ______.
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Mut H and Mut S
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In DNA replication, chain growth is in which direction?
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5' --> 3'
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Replication of DNA initiates at _________ and proceeds in both directions from there:
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Origin of Replication
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DNA synthesis is initiated with what kind of primer? What synthesizes this primer?
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RNA primer
Primase |
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Which two polymerases play a role in normal DNA replication in bacteria?
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Pol I and Pol III
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Which bacterial DNA polymerase removes RNA primers and replaces them with DNA (has both 5'-3' exonuclease and polymerase activity)?
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Pol I
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What is the major replicating enzyme of bacterial DNA?
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Pol III
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What carries out primer synthesis in eukaryotes?
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Pol alpha
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Unwinds the DNA double helix:
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DNA helicase
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Relieves the torsional strain in DNA from the unwinding:
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Topoisomerase
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Type of reaction involved in topoisomerase relieving the torsional strain:
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transesterfication
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Name the two enzymes (one in bacteria, one in eukaryotes) that remove RNA primers
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DNA Pol I (bacteria)
Fen I (eukaryotes) |
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What acts as the sliding clamp in DNA replication in eukaryotes? In bacteria?
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PCNA (eukaryotes)
Beta subunit of DNA Pol III (bacteria) |