Term
| If the E.coli DNA had incorporated 2-aminopurine and bromodeoxyuridine and was unable to repair its DNA, the midpoint melting temperature of this DNA would be ______ than DNA from an E.coli strain that was repair-proficient |
|
Definition
|
|
Term
| During mismatch repair by DNA polymerase I, ____ are incorporated from ____ substrates and _____ are removed |
|
Definition
|
|
Term
| What are the major polymerases involved in replicating DNA? |
|
Definition
1)DNA polymeraseIII holoenzyme in E.coli
2)DNA pol delta in Eukaryotes |
|
|
Term
| The ___ and _____ in Eukaryotes perform similar functions and are an example of convergent evolution |
|
Definition
| Beta clamp in E.coli & PCNA in eukaryotes |
|
|
Term
| What unwinds DNA during replication in E.coli and Eukaryotes? |
|
Definition
1)DnaB helicase in E.coli
2)MCM in eukaryotes |
|
|
Term
| In E.coli RNA polymerase which subunit appears to be essential for assembly and activation of RNA polymerase by regulatory proteins |
|
Definition
|
|
Term
| In E.coli under what conditions will catabolite activator protein be active and lac repressor inactive, resulting in increased transcription of the lac operon? |
|
Definition
| high lactose, low glucose |
|
|
Term
| What to tRNA synthetases do? |
|
Definition
| covelantely attach the proper amino acid to a specific tRNA molecule by recognizing specific bases in the acceptor stem, anticodon stem, or anticodon of tRNAs. |
|
|
Term
| When does a given sample of DNA absorb more ultraviolet light |
|
Definition
| when it becomes denatured |
|
|
Term
| What is the Wko value for a relaxed duplex circular DNA |
|
Definition
|
|
Term
| Palindromic nucleotide sequences in duplex DNA cause form ____ |
|
Definition
|
|
Term
| The conservation of secondary structures in ribosomal RNA suggests that .... |
|
Definition
| these secondary structures are functionally important |
|
|
Term
| All DNA polymerases including reverse transcriptase, incorporate what in the 5` to 3` direction |
|
Definition
| deoxynucleoside monophosphates |
|
|
Term
| The E.coli ribosome has how many binding sites for tRNA? |
|
Definition
|
|
Term
| During the initiation of protein synthesis, what binds to the P-site? |
|
Definition
|
|
Term
| In the initiation of DNA replication cycle in eukaryotes, what is present at replicators throughout the cell cycle? |
|
Definition
|
|
Term
| What is ORC bound by in the DNA replication process of Eukaryotes? |
|
Definition
| Cdc6p and MCM proteins during the initiation stage |
|
|
Term
| What is the enzyme that synthesizes DNA using a viral RNA as a template? |
|
Definition
|
|
Term
| What assists in protein folding by binding to hydrophobic regions exposed in an unfolded or partially folded protein? |
|
Definition
| DnaK (or Hsp70 in Eukaryotic cells) |
|
|
Term
| How many codons can encode a specific amino acid and why |
|
Definition
| more than one, because the genetic code is degenerate |
|
|
Term
| EF-Ts is bound to tRNA is similar in structure to ____ supporting the idea of molecular mimicry |
|
Definition
|
|
Term
| What makes the translational initiation factor unavailable for protein synthesis |
|
Definition
| Phosphorylation of elF-2alpha |
|
|
Term
| For proteins that bind to DNA via helix-turn-helix motif, what is in the turn to provide flexibility? |
|
Definition
| a conserved glycine residue |
|
|
Term
| What general transcription factor for RNA polymerase II acts immediately after TFIID in the formation of the pre-initiation complex? |
|
Definition
|
|
Term
| What is a general transcription factor for RNA polymerase II that binds specifically to enhancer sequences |
|
Definition
|
|
Term
| What stimulates transcription of the araBAD operon? |
|
Definition
| AraC protein bound to arabinose and two two separate sites in the araBAD promoter region. |
|
|
Term
| What does transposase do? |
|
Definition
1) mediates the insertion of a transposon at the target site in DNA by introducing staggered cuts at the target site.
2) then inserts the trasposon at the target site by joining each 3` end of the transposon to the 5` ends of the target site. |
|
|
Term
| In E.coli what region is complemetary to the Shine-Delgarno seq. of the mRNA |
|
Definition
| a region near the 3` end of 16S rRNA |
|
|
Term
| In DNA repair what does the methyl directed mismatch repair system do? |
|
Definition
| distinguishes the parental DNA strand of duplex DNA because it is methylated, then repairs the DNA lesion in the other strand that is not methylated. |
|
|
Term
| In the Holliday model DNA recombination between one duplex DNA carrying genes XYZ and anotoher duplex DNA containing genes xyz can produce what that has what? |
|
Definition
| can produce a heteroduplex DNA that has information for genes XYZ in one strand and XyZ in the other DNA strand |
|
|
Term
|
Definition
| a stress hormone that decreases protein synthesis and promotes protein breakdown. |
|
|
Term
|
Definition
| aplha-ketogluterate and aspartate |
|
|
Term
| What produces thymine dimers. What repairs them? |
|
Definition
| UV irradiation causes covalent bonds to form between adjacent thymines in DNA. Photolyase repairs them by breaking these covalent bonds. |
|
|
Term
| The promoter sequences of E.coli RNA polymerase contain what 2 seq. elements |
|
Definition
|
|
Term
| What is Rho? and what does it do |
|
Definition
| an ATP- dependent helicase that terminates transcription by running into and disrupting the complex of RNA polymerase still bound to both the DNA and transcript that is has synthesized. |
|
|
Term
| What does the Lac repressor do? |
|
Definition
| inhibits expression of the lac operon by binding to a specific seq. named the lac operator in the promoter region of the lac operon. |
|
|
Term
| what does CAP (catabolite activator protein) do and what does it bind to |
|
Definition
| bound to cAMP,stimulates transcription of the araBAD operon by binding to the CAP binding site that is near the RNA polymerase binding site to assist in formation of the closed promoter complex |
|
|
Term
| After formation of the filament of RecA molecules bound to single-stranded DNA, what does this nucleoprotein complex do? |
|
Definition
| promotes base pairing between the single-stranded DNA in the RecA filament and its homologous seq in duplex DNA. |
|
|
Term
| what are telomeres and where are they located |
|
Definition
| located at the ends of eukaryotic chromosomes, are short tandenly repeated sequences. In somatic cells the repeated sequences are progressively lost with each cell division. |
|
|
Term
| what is semiconservative and what process associates with it |
|
Definition
| DNA replication is semiconservative and each strand of the parental DNA acts as the template for the synthesis of the complementary progeny DNA strand. |
|
|
Term
| how is E.coli DNA polymerase I processivity compared to E.coli DNA polymerase III holoenzyme? |
|
Definition
| E.coli DNA polymerase I is not very processive compared to enormously processive E.coli DNA polymerase III holoenzyme. |
|
|
Term
| what is the beta dimer of E.coli DNA polymerase III holoenzyme called? What does the central cavity do? |
|
Definition
| sliding clamp, central cavity large enough to accomidate duplex DNA |
|
|
Term
|
Definition
| (Origin recognition complex) a eukaryotic origin in DNA replication is recognized and bound by this |
|
|
Term
| what is RuvA bound to a Holliday junction necessary for? |
|
Definition
| branch migration of the holliday junction |
|
|
Term
| What happens what tryptophan is scarce? |
|
Definition
| the ribosome pauses at one of two codons corresponding to tryptophan in the leader transcript, leading to the formation of the 2:3 antiterminator hairpin |
|
|
Term
| In the DNA polymerases general right hand structure what does the fingers domain recognize? |
|
Definition
|
|
Term
|
Definition
| a specific transcription factor that binds to an enhancer seq named "Octamer" |
|
|
Term
| What does the mediator interact with in transcription? |
|
Definition
| the CTD of RNA polymerase II |
|
|
Term
| Phosphorylation of serine residues in the N-terminal tail of hisone H3 leads to what |
|
Definition
| remodeling of the chromatin |
|
|
Term
| Where are inteins found and when are they removed? |
|
Definition
| found in the coding regions of genes, removed during protein splicing. |
|
|
Term
| In the processing of primary transcript synthesized by eukaryotic RNA pol II , what does guanylyl transferase do? |
|
Definition
| joins the alpha phosphate of GTP to the beta phosphate of the 5` terminal nucleotide of the primary transcript |
|
|
Term
| Is the C-terminal domain of one of the subunits of yeast RNA pol II phosphorylated when the polymerase first assembles at the promoter? |
|
Definition
|
|
Term
| What is reverse transcriptase |
|
Definition
| an RNA directed DNA polymerase |
|
|
Term
| what do transcription factors do in eukaryotic RNA pol II |
|
Definition
| bind to enhancer seq. in promoters ,stimulate transcription via loop method. |
|
|
Term
| Can one amino acid be coded by more than one codon |
|
Definition
|
|
Term
| what does a DNA binding protein containing a leucine zipper motif have |
|
Definition
| a leucine residue at every seventh amino acid |
|
|
Term
| what happens in the absence of arabinose |
|
Definition
| araC protein acts as a repressor for the araBAD operon by binding to two sites in the promoter region. A DNA loop separates the two DNA sites. |
|
|
Term
| What binds to the -35 region of the promoter |
|
Definition
| The sigma subunit of E.coli RNA polymerase |
|
|
Term
|
Definition
| binds N-formyl-methonyl tRNA during the initiation of protein synthesis in E.coli |
|
|
Term
| During the intiation of protein synthesis in E.coli what occupies the P-site |
|
Definition
| the N-formyl-methonyl tRNA |
|
|
Term
|
Definition
| participates directly at the step of translocation of the ribosome on the mRNA |
|
|
Term
|
Definition
| cleaves the Holliday junction |
|
|
Term
| How can point-mutations occur |
|
Definition
| by natural processes, the adenine base in DNA may tautomerize to cause its innappropriate base pairing with the wrong nucleotide during DNA replication. |
|
|
Term
| what does CAP (catabolite activator protein) do |
|
Definition
| stimulates the binding of RNA polymerase to the lac promoter |
|
|
Term
| If a duplex circular DNA is 400 base pairs long and delta L=-4 what does that mean |
|
Definition
| This DNA is neither relaxed nor positively supercoiled |
|
|
Term
| what are conserved sequences |
|
Definition
| RNA sequences at the 5` end and the 3` end of an intron |
|
|
Term
| What does a class II aminoacyl tRNA synthetase do? |
|
Definition
| covalently joins the amino acid to the 3`-OH of the terminal nucleotide in the acceptor stem of a tRNA molecule. |
|
|
Term
| If Meselson and Stahl analyzed the seperate strands of DNA instead of duplex DNa after one round of DNA replication, they would have found what? |
|
Definition
| single stranded DNAs that were heavy in density and light in density |
|
|
Term
| what does the 5`-3` exonuclease of DNA polymerase I do? |
|
Definition
| removes the primer use to prime the synthesis of an Okazaki fragment in E.coli |
|
|
Term
| what happens when a DNA gyrase introduces negative supercoils in a duplex circular DNA molecule? |
|
Definition
| the enzyme binds to a cross-over point between two duplex DNAs, cleaves one duplex DNA and passes the other intact duplex DNA through the transient break. |
|
|
Term
| what subunit of DNA polymerase III holoenzyme has the DNA polymerase activity? |
|
Definition
|
|
Term
| What does RNA polymerase II do |
|
Definition
| recognizes promoters that often but do not always contain a TATA box in the promoter region. |
|
|
Term
| Rho is a helicase dependent on what |
|
Definition
|
|
Term
| At and near the replication fork in E.coli what does the DNA helicase, primase, and the two equiv of DNA polymerase III holoenzyme do? |
|
Definition
| DNA helicase unwinds the parental DNA, primase forms primers for Okazaki fragment synthesis, two equivalents of DNA polymerase III holoenzyme synthesize leading and lagging strands. |
|
|
Term
| What does the adenine of the 23S rRNA larege subunit of the E.coli ribosome do |
|
Definition
| abstracts a proton from the alpha amino group of the A-site aminoacyl tRNA |
|
|
Term
| what subunit of DNA polymerase III holoenzyme has the DNA polymerase activity? |
|
Definition
|
|
Term
|
Definition
| binds to the aminoacyl-tRNA and delivers it to the A site of the ribosome |
|
|
Term
| How does the 30S subunit of the ribosome bind to the mRNA |
|
Definition
| an interaction between Shine-Delgarno seq. in the mRNA and a complementary seq. in the 16S rRNA of the small ribosomal unit. |
|
|
Term
| Class I and 2 tRNA syntheses recognize what |
|
Definition
| specific parts of tRNAs, including the nucleotides in the acceptor stem, nucleotides in the anticodon loop, and nucleotides in the arms containing the D-loop and the tyc loop |
|
|
Term
| codons represent what, and three codons are |
|
Definition
| a specific amino acid. three codons are stop codons. |
|
|
Term
| in splicing what binds to the branch site? |
|
Definition
| U2snRNP binds there where the 5` end of the intron is joined to the 2`-OH of a conserved nucleotide in the branch site. |
|
|
Term
| what is a codon, what is codon recognition achieved by? |
|
Definition
| a group of 3 bases that codes for one amino acid, all have meaning, codon recognition achieved by aminoacyl tRNAs |
|
|
Term
|
Definition
| the appropriate amino acyl tRNA reads the codon through base pairing. |
|
|
Term
what is a stop (nonsense) codon
what does it result in |
|
Definition
when mutations alter a sense codon to –UAA,UAG,or UGA.
o Result in premature termination of protein synthesis and release of truncated (incomplete) proteins. |
|
|
Term
| general features of the genetic code |
|
Definition
genetic code is a triplet code, read from a fixed starting point in each mRNA
- the code is not overlapping
-All codons have meaning
-the genetic code is degenerate in most cases,each amino acid can be coded for by any of several triplet codons
-the base sequence is read from a fixed starting point without punctuation
-genetic code is “universal”
-composed of 3 nucleotides
-minimum genetic code set at 3
-3 stop codons
-every other combination of 3 corrisponds to a partic Amino Acid. |
|
|
Term
|
Definition
| when multiple ribosomes can translate the same mRNA at a given time |
|
|
Term
| 5` terminal methyl-GTP cap |
|
Definition
| essential for mRNA binding by eukaryotic ribosomes & enhances stability of mRNAs by preventing degradation by 5` exonucleases. |
|
|
Term
| 3` terminal poly (A) tail |
|
Definition
| enhances stability & translational efficiency of eukaryotic mRNAs |
|
|
Term
|
Definition
| an aminoglycoside antibiotic induces mRNA misreading. Resulting mutant proteins slow the rate of bacterial growth |
|
|
Term
|
Definition
| binds at the A site of both prokaryotic and eukaryotic ribosomes, accepting the peptide chain from the P site, terminating protein synthesis |
|
|
Term
|
Definition
EF-Tu-(5% of total protein in E.coli) G protein that binds aminoacyl-tRNA
and delivers it to the A site, can bind any amino-acyl-tRNA and deliver it to
the ribosome in a GTP-dependent reaction
EF-Ts-Guanine nucleotide exchange factor (GEF) that replaces GDP on EF-Tu
with GTP,recycles EF-Tu by exchanging GTP for GDP
EF-G-G protein that promotes translocation of mRNA, catalyzes GTP dependent translocation.
EF-Tu & EF-G compete for binding to ribosomes, t-RNA complexes
remarkably similar |
|
|
Term
| Chain elongation can be divided into 3 steps |
|
Definition
1) Codon-directed binding of the incoming aminoacyl tRNA at the A site. Decoding center regions of 16s rRNA make sure proper aminoayl-tRNA is in the A site
2) Peptide bond formation: transfer of the peptidyl chain from the tRNA bearing it to the-NH2 group of the new amino acid.
3) Translocation of the “one residue-longer” peptidyl-tRNA to the P site to make room for the next aminoacyl-tRNA at the A site. These shifts are coupled with movement of the ribosome one codon further along the mRNA. |
|
|
Term
|
Definition
recognized by E.coli ribosomes, these seq. lie about 10
nucleotides upstream from their AUG initiation codon, & are complementary to the UCCU core seq element of E.coli 16s rRNA |
|
|
Term
| E.coli initiation factors |
|
Definition
-IF-1- binds to 30s A site and prevents tRNA binding
IF-2- G- protein that binds fMet-tRNA, interacts with IF-1
IF-3 Binds to 30s E site, prevents 50s binding |
|
|
Term
| What is initiation elongation and termination |
|
Definition
Initiation – biding of mRNA and initiator aminoacyl-tRNA to small subunit,
followed by binding of large subunit
-Elongation-movement of ribosome along mRNA & synthesis of all peptide bonds- with tRNAs bound to Acceptor (A) and peptidyl (P) sites
-Termination-when stop codon is reached |
|
|
Term
|
Definition
-proposed by Francis Crick for codon anti-codon pairing
-hypothesized that the first two bases of the codon and the last two bases of the anticodon form canonical Watson-Crick base pairs.
-pairing between the third base of the codon & first base of the anticodon follows less stringent rules, which is why there is a wobble in base pairing at this position
-this leads to more base pairing possibilities at the Third position of the codon. |
|
|
Term
| two classes of aminoacyl tRNAs |
|
Definition
Class I-aminoacyl tRNA synthetases first add the amino acid to the 2`-OH of
the terminal adenylate residue of tRNA before shifting it to the 3-OH
-Class II- enzymes add it directly to the 3`-OH |
|
|
Term
| Semi-conservative DNA replication |
|
Definition
| one of the two original strands is conserved in each progeny molecule. |
|
|
Term
| Semi-discontinuous DNA replication |
|
Definition
| the lagging strand is formed from Okazaki fragments which are joined to form the final product. |
|
|
Term
|
Definition
1)template
2)primer that provides 3`OH end that extends by DNA polymerization
3)synthesizes 5`to 3` end |
|
|
Term
| DNA Polymerase I (Pol I)- |
|
Definition
catalyzes 20 cycles of polymerization before the new strand dissociates from the template .
- 20 cycles constitutes moderate “processivity” number of nucleotides added by a DNA polymerase)
- nucleotides are added to the 3` end of the strand.
- Has ability to nick translate by concurrent activities of
- Excises the primer (removes primer) |
|
|
Term
| 3` to 5` exonuclease of DNA polymerase |
|
Definition
removes nucleotides from the 3` end of the chain-serves as a proofreading function
-exonuclease removes incorrectly matched bases so polymerase can try
again.
-newly-formed strand oscillates between the polymerase and 3`exonuclease
sites, adding a base and then checking it. |
|
|
Term
|
Definition
5` Exonuclease activity working together with polymerase, accomplishes this.
- plays an important role in primer removal during DNA replication |
|
|
Term
|
Definition
the polymerase that carries out replication in E.coli
-uses RNA primer
-atleast 10 diff subunits
-“core “enzyme has 3 subunits, alpha, epsilon and theta
-alpha-has polymerase activity
-Epsilon (has proofreading exonuclease, is a 3` exonuclease)
-Theta ( glue, keeps core assemply together, involved in holoenzyme
assembly)
-has beta clamp (beta subunit dimer forms ring around DNA, sliding clamp, makes
enzyme highly processive)
-has gamma complex
DNA polymerase III holoenzyme |
|
|
Term
| Leading and Lagging strand synthesis- |
|
Definition
- Lagging strand synthesis requires repeated priming
o Primase bound to the DnaB helicase carries out this function, periodically forming new RNA primers on the lagging strand
-DNA synthesis proceeds in the 5`to 3` direction, because the template strand is read in the 3`to 5` direction .
- All single-stranded regions of DNA are coated with SSB ( single stranded bonding protein)
-Leading strand is formed continuously
- Lagging strand is formed from Okazaki fragments |
|
|
Term
|
Definition
are joined to form the final product.
- The lagging strand is formed from these, it copies in these segments |
|
|
Term
|
Definition
- M-phase- phases of mitosis and cell division
- G1- typically longest part of cell cycle, rapid growth and metabolic activity
- G0-phase that cells which are not growing and dividing are stuck in (neurons)
- G2- short period of growth when cell prepares for division
- Progression regulated by checkpoints
-depend on cyclins and cyclin dependent kinases (CDKs)
- Initiation of replication depends origin recognition complex (ORC)
- DNA replication occurs only once per cell cycle
-Initiation of DNA replication divided in 2 steps
-1)licensing of replication origins
2) activation of replication at origin during S phase by action of Cdc7-
Dfb4 and S-Cdk (S phase cyclin-dependent kinases |
|
|
Term
|
Definition
RNA-dependent DNA polymerase
-maintains telomere length by restoring telomeres at the 3` ends of chromosomes
-Uses RNA to dictate synthesis of repeat seq. |
|
|
Term
|
Definition
-Transcribes the RNA template into a complementary cDNA strand to form a DNA:RNA hybrid. -Has 3 enzyme activities
1) RNA-directed DNA polymerase activity
2) RNase H activity ( an exonuclease activity that degrades RNA chains in
DNA: RNA hybrids)
3)DNA-directed DNA polymerase activity (replicates the ssDNA remaining
after RNase H degradation of the viral genome , yielding a DNA duplex) which
directs the remainder of the viral infection process. |
|
|
Term
| Two possible point mutations |
|
Definition
Transitions (one purine or
pyrimidine for another) 2) Transversions ( a pyrimidine for a purine, or vice versa) |
|
|
Term
|
Definition
Change the sequence of bases in DNA either by
-Substitution of one base pair for another (so called point-mutations)
-Point mutations arise when base pairs with an inappropriate partner |
|
|
Term
| Mutations can be induced by base analogs |
|
Definition
-5-bromouracil
-2-aminopurine
-or oxidation; alkylation |
|
|
Term
|
Definition
a. Pyrimidine dimmers can be repaired by this
b. Repairs thymine dimmers, breaks cyclobutyl ring. |
|
|
Term
|
Definition
a. DNA glycosylase removes damaged base , creating an apurinic or “AP” site
b. A damaged base is excised from the sugar-phosphate backbone by DNA glycosylase , creating an AP site. Then an AP endonuclease severs the DNA strand, and an excision nuclease removes the AP site and several nucleotides. DNA polymerase I and DNA ligase repair the gap. |
|
|
Term
| 2) Methyl –directed mismatch repair |
|
Definition
a. Scan DNA duplexes for mismatched bases, excise the mispaired region and replace it by DNA polymerase-mediated local replication
b. E.coli is an example
c. Methlyation occurs post-replication, repair proteins identify methylated strand as parent, remove mismatched bases on other strand and replace them.
d. System recognizes mistake on top strand b/c has not yet been methylated, removes wrong base and replaces with correct one |
|
|
Term
| SB repair : KU70/89, homologous recomb |
|
Definition
a. Binds the ends & recruits a set of proteins that juxtaposes the broken ends. Processing of the ends to generate proper substrates for ligase IV then occurs, followed by DNA-ligase mediated end joining.
b. KU 70/80 mediates homologous DNA end joining
c. Double-strand breaks that arise during the S phase of the cell cycle
d. can be repaired through homologous recombination, which creates a D-loop and sister chromatid-directed DNA replication restores the info content of the damaged duplex, depending on how the holliday junctions are resolved, the products are either noncrossover or crossover. |
|
|
Term
|
Definition
- binds single stranded DNA forming a nucleoprotein filament capable of strand invasion and homologous pairing.
- Also known as recombinase,
- Is a multifunctional protein for general recombination
- Mediates the ATP-dependent DNA strand exchange reaction, leading to formation of the Holliday junctions
- Forms a right-handed helical filament with six monomers per turn, with each monomer spanning about 3 nucleotides of DNA
- The RecA nucleoprotein filament is a scaffold upon which recombination takes place
o The filament has a deep grove large enough to encompass 3 strands of DNA. |
|
|
Term
|
Definition
| Duplexes partially unwind, and free, single-stranded end of one duplex begins to base pair with its nearly complementary single-stranded region along the intact strand in the other duplex. (process called strand invasion) Ligation follows forming Holliday junction. |
|
|
Term
|
Definition
recombination involving similar DNA
Sequences |
|
|
Term
| Non-homologous recombination |
|
Definition
recombination involving very different
Nucleotide sequences |
|
|
Term
|
Definition
the enzymatic insertion of a transposition (mobile segment
of DNA) |
|
|
Term
|
Definition
the process of underlying homologous
Recombination
-Requires breakage& reunion of DNA strands. |
|
|
Term
|
Definition
| family of enzymes involved in base excision repairhey remove the damaged nitrogenous base while leaving the sugar-phosphate backbone intact, creating an apurinic/apyrimidinic site, commonly referred to as an AP site. This is accomplished by flipping the damaged base out of the double helix followed by cleavage of the N-glycosidic bond. |
|
|
Term
|
Definition
| cleaves phosphate ester backbone of DNA |
|
|
Term
| Nucleotide excision repair |
|
Definition
| discontinuing enlarged by excision endonuclease & DNA polymerase fills in. DNA ligase seals discontinuing. |
|
|
Term
| What does DNA polymerase I require |
|
Definition
1)template
2)primer that provides 3`OH end that extends by DNA polymerization
3)stynthesize 5` to 3` end |
|
|
Term
how many subunits does DNA pol III have?
what are the 3 sub-assemblies of the "core" enzyme |
|
Definition
Alpha-is polymerase
Epsilon-3` endonuclease
Theta-subunit involved in holoenzyme assembly and epsilon subunit stablization, glue, keeps core assembly together.
beta-forms a ring around DNA,responsible for synthesizing strand
gamma complex |
|
|
Term
| All single-stranded regions of DNA are coated with what? |
|
Definition
| SSB (single-stranding binding protein) stablizes single strand DNA unwound by helicase |
|
|
Term
| what does DNA gyrase do in DNA replication |
|
Definition
| relieves tortion that accum. by virtue of helicase unwinding of duplex |
|
|
Term
|
Definition
| Initiation factor, origin binding protein |
|
|
Term
|
Definition
| replicative helicase, 5 to 3` helicase (DNA unwinding) |
|
|
Term
|
Definition
| DnaB chaperone loading DnaB on DNA |
|
|
Term
|
Definition
|
|
Term
| DNA polymerase III holoenzyme |
|
Definition
| Elongation ( DNA synthesis) |
|
|
Term
|
Definition
| covalently links okazaki fragments |
|
|
Term
| DNA polymerase uses 2 metals |
|
Definition
1)one metal helps active 3` hydroxyl to make better nucleophile
2)Other metal facillitates nucleotide hydrolysis |
|
|
Term
| Using the right hand structure of DNA polymerases what does the palm fingers and thumb represent? |
|
Definition
Palm domain-active site lies in crevice
Fingers-act in deoxynucleotide recognition and binding
Thumb-responsible for DNA binding |
|
|
Term
| What do familes A B C X and Y include of DNA polymerases |
|
Definition
Family A-polymerases involved in DNA repair in bacteria
Family B-the eukaryotic polymerases involved in replication of the chromosomal DNA
Family C-bacterial chromosome DNA- replicating enzymes.
Fmailes X and Y- act in DNA repair pathways |
|
|
Term
| what happens in G1 of the cell cycle |
|
Definition
| cells license there genomes to become duplicated |
|
|
Term
| Where are genomes duplicated in the cell cycle |
|
Definition
|
|
Term
| what are the two steps of initiation of DNA replication |
|
Definition
1) licensing of replication origins, involves highly regulated assembly of initiation control proteins at the ORC to form prereplication complexes (pre-RCs)
2) activation of replication at the origins during S phase by the action of Cdc7-Dbf4 and S-CDK |
|
|
Term
| What are MCMs i eukaryotic cell replication |
|
Definition
| replication licensing factors. |
|
|
Term
| What are the steps in Eukaryotic DNA replication |
|
Definition
1)ORC binds to replication site
2)Cdc6 and Cdt1 and MCM are recruited
3)phosphorylation mediated by S-CDK and Cdc-7 Dbf4
4)phosphorylation of MCM and binding of Cdc45 activates helicase activity of MCM
5)phosphorylation of Sld2 and Sld3 (interact with Dpb11) recruit polymerase to the origins |
|
|
Term
| What proteins of the eukaryotic pre replication complex are ATP dependent |
|
Definition
|
|
Term
|
Definition
| inhibits DNA replicaiton by preventing the incoporation of MCM complexes into the pre-RC |
|
|
Term
| what are the 2 major replicative DNA polymerases in eukaryotic cells? |
|
Definition
1)polymerase delta
2)polymerase Epsilon |
|
|
Term
| What is structurally analogous to the Beta dimer (sliding clamp) in prokaryotic cells? |
|
Definition
|
|
Term
| what does general recombination involve |
|
Definition
| breakage and reunion of DNA strands, involves exchange of DNA segments |
|
|
Term
| What enzyme complex initiates recombination, how does it work |
|
Definition
RecBCD, composed of Rec B, Rec C, and Rec D. has both helicase and nuclease activity
1) initiates recombination by attaching to the end of a DNA duplex and using its helicase function to unwind dsDNA
2) as it unwinds DNA, SSB binds to single strands
3)RecBCD endonuclease activity cleaves ssDNA and directs binding of RecA to 3`-terminal strand
4)a nucleoprotein is formed (Rec A filament) which is capable of pairing with dsDNA and strand invasion. |
|
|
Term
| which type of strands exchange information during DNA recombination |
|
Definition
| strands with like polarity |
|
|
Term
| what is branch migration mediated by ? |
|
Definition
|
|
Term
| How are double strand breaks repaired during the S phase of the cell cycle |
|
Definition
|
|
Term
| nirtrous acid converts cytosine to ___ and adenine to _____ |
|
Definition
|
|
Term
| In transcription what happens |
|
Definition
| all RNAs are synthesized from DNA templates by DNA-dependent RNA polymerases |
|
|
Term
| In transcription how does the polymerase move across the DNA strand, and how does it grow |
|
Definition
| moves across 3`-5` ,grows 5` to 3` |
|
|
Term
| What makes the polymerase reaction in transcription thermodynamically favorable |
|
Definition
| Hydrolysis of PPi to inorganic phosphate by pyrophosphatses |
|
|
Term
| How is transcription initiated in prokaryotes |
|
Definition
| by RNA polymerase holoenzyme, with the subunit composition of apha2beta beta` sigma |
|
|
Term
| What is the core polymerase in transcription |
|
Definition
|
|
Term
| binds of what allows the polymerase in transcription to recognize differenct DNA seq. that act as promoters |
|
Definition
|
|
Term
| what are promoters in transcription |
|
Definition
| nucleotide sequences that idnetify the location of transcription start sites, where transcription begins |
|
|
Term
| Without sigma bond what can happen |
|
Definition
| the core polymerase can transcribe DNA into RNA, but cannot innitate transcription |
|
|
Term
| what is the template strand |
|
Definition
| the strand of duplex DNA that is read by RNA polymerase in the 3` to 5` direction so the RNA product, the transcript grows in the 5` to 3` direction |
|
|
Term
| what is the nontemplate strand |
|
Definition
| the strand not read by RNA polymerase |
|
|
Term
| RNA transcript has the same chemical sense as what |
|
Definition
|
|
Term
| what is the equation for the probability that the enzyme can dissociate from promoter |
|
Definition
| Kd= (RNAD) (promoter)/(RNA*promoter)=10^-6 or 10^-9 |
|
|
Term
| what forms the closed promoter complex in transcription |
|
Definition
| RNA polymerase holoenzyme and promoter (DNA not unwound) Kd=10^-6 or 10^-9M |
|
|
Term
| What are the two consensus seq. in the promoter of prokaryotic cells |
|
Definition
| Pribnow box(near-10 with consensus TATAAT, region ideal for unwinding because rich in As and Ts which form 2 H bonds per base pair), -35 region(consensus TTGACA-sigma subunit appears to bind here) |
|
|
Term
| what recognizes the pribnow box & -35 region to allow RNA polymerase to form the closed complex |
|
Definition
|
|
Term
| what is the elongation enzyme in prokaryotic cells |
|
Definition
| The core polymerase (without sigma) |
|
|
Term
| how many binding sites does RNA polymerase have for NTPs |
|
Definition
two
1) intiation site-prefers to bind ATP and GTP
2)elongation site-binds the second incoming NTP |
|
|
Term
| What are the two types of transcription termination in bacteria |
|
Definition
1)RHO
2)intrinsic-determined by termination sites, consisting of inverted repeats, irch in G:C which form a stem-loop structure in RNA transcript, a non repeating seg that punctuates the inverted repeats, a run of 6-8 As in the DNA template coding for Us in transcript |
|
|
Term
|
Definition
| at various positions relative to the promoter, upstream or downstream |
|
|
