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saunde86
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describe what the phrase "semi-conservative DNA replication" means.
one of each original strand is conserved in each progeny molecule
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describe what "semi-discontinuous" DNA replication means.
the leading strand is replicated continuous and the lagging strand is replicated with okazaki fragments in a discontinuous fashion.
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what unwinds the double helix?
helicase
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what molecule compensates for DNA supercoiling?
DNA gyrase
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when DNA pol I is described to catalyze 20 cycles of polymerization, what does this mean?
this means that on average it will add 20 nucleotides to the growing molecule
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what is processivity
processivity is the term that describes how well a polymerase synthesizes a DNA/RNA chain, add x amounts of bases
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what is the role of the 3' to 5' exonuclease of DNA pol I
serves as a proofreading function to remove incorrect bases
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describe the process of nick translation
occurs because of the 5'-nuclease acitivity working together with the polymerase to degrade the primer and fill in behind with bases to move to "nick" along
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why is DNA pol III holoenzyme considered the "real" DNA polymerase in E.coli?
this is the real workhorse because it has a processivity of around 5 million bases
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what is the role of the Beta subunit of DNA polymerase III holoenzyme
the beta dimer forms a ring around DNA to attach the core to do activity also called the beta clamp. could account for the huge processivity
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what are the differences between leading and lagging strand synthesis
lagging strand synthesis requires repeated priming for okazaki fragments to be synthesized.
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what are okazaki fragments and their significance in semi-discontinuous strand synthesis
they are pieces of synthesized DNA of the lagging strand that needed to be joined together during nick translation
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what is included in the A family of polymerases?
polymerases involved in DNA repair in bacteria
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what is included in the B family of polymerases?
polymerases involved in replication of the eukaryotic chromosome
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what is included in the C family of polymerases?
polymerases involved in the replication of the bacterial chromosome
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what do the families X and Y include as far as polymerases?
they contain polymerases that act in DNA repair pathways
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what does the RT family contain?
this is the family that designates retrovirus polymerases
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what are the different phases of the cell cycle
G1 phase, S phase where chromosomal duplication happens, G2 phase and mitosis
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what is a CDK
a cyclin dependant kinase
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what does ORC stand for?
origin recognition complex
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what activates replication?
the actions of Cdc7-Dbf4 and S-CDK
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compared eukaryotic DNA polymerase delta to E coli DNA polymerase III holoenzyme in terms of subunit assemblies and their functions
they are both the principal DNA replicases,
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what does the ORC help to form?
a prereplication complex
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what proteins are recruited by the ORC after it binds the origen?
Cdc6, Ctd1 and MCM proteins
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what is important, energy wise of the forming of the pre-RC?
it is energy dependant
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what is geminin? and what is its function
it is a molecule that inhibits replication by preventing the incorporation of MCM complexes into the pre-RC
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what is PCNA and what is its association with DNA synthesis?
PCNA associates with the delta polymerase to assist with the high processivity, (is homologous with the beta sliding clamp)
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what is the function of telomerase and why is it important
maintains telomere length by restoring telomeres at the 3' ends of chromosomes
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what is unusual about reverse transcriptase
it transcribes the RNA template into a complementary cDNA strand to form an RNA DNA hybrid
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what is a mutation
a change in nucleotides, can be due to a mistake intranscription
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what is the RecBCD complex's function?
it initiates recombination has both helicase and nuclease activity
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what is important about energy with recombination?
it is an ATP-dependent action
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how are different DNA adducts repaired
- mismatch repair
- base excision repair
- nucleotide excision repair
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how does RecA protein act in DNA recombination
it forms a nucleoprotein filament capable of strand invasion and homologous pairing
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what is a holliday junction
the holliday junction is the point at strand invasion during recombination where the strands cross
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what proteins recognize the holliday junction and how do they act
RuvA and RuvB recognize and bind to the holliday junction to help process it, A acts as a branch site and B acts as the supercoiling compensator
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what is genetic recombination of DNA
it is the shuffling of genetic homologs within DNA
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why is recombination of DNA important
it adds to genetic diversity
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what is a prion?
a protein that acts as a genetic agent
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what is the functional importance of the classes of RNA, mRNA, tRNA and rRNA respectively
- mRNA is the actual RNA that encodes for proteins
- tRNA is the RNA molecule that transports bound nucleotides to be part of the chain
- rRNA is the ribosomal RNA that assists with translation
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what is a primary transcript
a primary transcript is a transcript that contains introns and exons
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what are the four stages in transcription?
binding, initiation, elongation and termination
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what is an open promoter complex
an open promoter complex is when the DNA is unwound and RNA polymerase is bound to the promoter
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what is a closed promoter complex
when RNA polymerase is bound to a promoter and DNA is not unwound
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what consensus sequencs motifs are in a bacterial promoter Pribnow box (-10), and the -35 region
pribnow box is rich in TA (TATAAT) to make it a nice area for unwinding due to weaker hydrgen binding forces and the -35 region has (TTGACA)
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describe the two mechanisms of chain termination in E. coli
- Chain termination: with Rho termination factor, ATP-dependent helicase unwinds the DNA:RNA hybrid and releases RNA chain
- intrinsic termination using stem-loop structure
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Alpha-amanitin is an octapeptide from Amanita phalloids and is poisonous. Why?
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what is an exon
an exon is a sequence of the RNA that codes for a gene
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what is an intron
an intron is an interrupting sequence
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what is the importance of alternative splicing
it leads to one gene being able to code for many proteins
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what is an anit-codon
part of a tRNA that reads the codon for amino acid placement
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what is a stop, or nonsense codon
untranslatable codon to signal the stop of protein synthesis
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what are the four general features of the genetic code
- the genetic code is triplet
- it is degenerate
- genetic code is universal
- has no punctuation is read continuously
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what are the animo-acyl tRNA sythetases, and how do they recognize tRNAs
they translate the genetic code, they recognize a tRNA by reading it through base pairing with its anti-codon loop
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what is the Shine-Delgarno sequence and what role does it play in prokaryotic translation
is a purine rich segment that the ribosome binds to
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how does elongation occur, what factors are involved, and is energy consumed?
the factors involved are elongation factors Tu and G GTP is consumed with these reactions
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what is the function of IF2, EF-Tu, and EF-G
both initiation factors act to shuttle amino acids to be incorporated, and IF2 delivers tRNA
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how do termination release factors work
they work to form a hydrolase to cleave the peptidyl chain from the tRNA carrier
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what is a polysome
is a RNA molecule with many ribosomes attached and working
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why are streptomycin and tetra cyclin useful antibiotics
block binding at the A site
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what is a chaperone
chaperones are proteins that help other proteins fold
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