Card Set Information
describe what the phrase "semi-conservative DNA replication" means.
one of each original strand is conserved in each progeny molecule
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.
what unwinds the double helix?
what molecule compensates for DNA supercoiling?
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
what is processivity
processivity is the term that describes how well a polymerase synthesizes a DNA/RNA chain, add x amounts of bases
what is the role of the 3' to 5' exonuclease of DNA pol I
serves as a proofreading function to remove incorrect bases
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
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
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
what are the differences between leading and lagging strand synthesis
lagging strand synthesis requires repeated priming for okazaki fragments to be synthesized.
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
what is included in the A family of polymerases?
polymerases involved in DNA repair in bacteria
what is included in the B family of polymerases?
polymerases involved in replication of the eukaryotic chromosome
what is included in the C family of polymerases?
polymerases involved in the replication of the bacterial chromosome
what do the families X and Y include as far as polymerases?
they contain polymerases that act in DNA repair pathways
what does the RT family contain?
this is the family that designates retrovirus polymerases
what are the different phases of the cell cycle
G1 phase, S phase where chromosomal duplication happens, G2 phase and mitosis
what is a CDK
a cyclin dependant kinase
what does ORC stand for?
origin recognition complex
what activates replication?
the actions of Cdc7-Dbf4 and S-CDK
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,
what does the ORC help to form?
a prereplication complex
what proteins are recruited by the ORC after it binds the origen?
Cdc6, Ctd1 and MCM proteins
what is important, energy wise of the forming of the pre-RC?
it is energy dependant
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
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)
what is the function of telomerase and why is it important
maintains telomere length by restoring telomeres at the 3' ends of chromosomes
what is unusual about reverse transcriptase
it transcribes the RNA template into a complementary cDNA strand to form an RNA DNA hybrid
what is a mutation
a change in nucleotides, can be due to a mistake intranscription
what is the RecBCD complex's function?
it initiates recombination has both helicase and nuclease activity
what is important about energy with recombination?
it is an ATP-dependent action
how are different DNA adducts repaired
base excision repair
nucleotide excision repair
how does RecA protein act in DNA recombination
it forms a nucleoprotein filament capable of strand invasion and homologous pairing
what is a holliday junction
the holliday junction is the point at strand invasion during recombination where the strands cross
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
what is genetic recombination of DNA
it is the shuffling of genetic homologs within DNA
why is recombination of DNA important
it adds to genetic diversity
what is a prion?
a protein that acts as a genetic agent
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
what is a primary transcript
a primary transcript is a transcript that contains introns and exons
what are the four stages in transcription?
binding, initiation, elongation and termination
what is an open promoter complex
an open promoter complex is when the DNA is unwound and RNA polymerase is bound to the promoter
what is a closed promoter complex
when RNA polymerase is bound to a promoter and DNA is not unwound
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)
describe the two mechanisms of chain termination in E. coli
: with Rho termination factor, ATP-dependent helicase unwinds the DNA:RNA hybrid and releases RNA chain
intrinsic termination using stem-loop structure
Alpha-amanitin is an octapeptide from Amanita phalloids and is poisonous. Why?
what is an exon
an exon is a sequence of the RNA that codes for a gene
what is an intron
an intron is an interrupting sequence
what is the importance of alternative splicing
it leads to one gene being able to code for many proteins
what is an anit-codon
part of a tRNA that reads the codon for amino acid placement
what is a stop, or nonsense codon
untranslatable codon to signal the stop of protein synthesis
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
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
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
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
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
how do termination release factors work
they work to form a hydrolase to cleave the peptidyl chain from the tRNA carrier
what is a polysome
is a RNA molecule with many ribosomes attached and working
why are streptomycin and tetra cyclin useful antibiotics
block binding at the A site
what is a chaperone
chaperones are proteins that help other proteins fold