BIOS 372 Ch. 28
[#] core polymerases are held together by [blank], and associate with each template strand by the [blank]. The [blank] (one g, one d, and one d' subunit) helps to load b onto DNA. The [3rd blank] is also called the clamp loader - it uses the energy from ATP [blank] to assemble a pair of b subunits on to each strand of DNA at the replication fork. This happens once on the [blank] strand. The core polymerase synthesizing the [blank] strand must release from the DNA at the end of each Okazaki fragment. The b-clamp is released by [blank], and then must be reloaded (using the [4th blank]) onto the next Okazaki fragment.
2, t, b-clamp, g-complex, hydrolysis, leading, lagging, t,
"end-replication problem" - DNA pol requires a [blank] on the previous nucleotide to extend the strand following excision of [blank] - at the extreme ends of each strand, no such [1st blank] exists The [2nd blank] at the [3 or 5?]' ends of each newly synthesized strand cannot be replaced by DNA b/c [blank] can only extend a strand.
3'OH, RNA primers, 5, DNAP
mutations- [blank] - examples: 5-BU is a thymine analog, pairs with guanine causing an A to G transition. The enol form of 5-BU can be incorporated in place of cytosine. If it returns to its keto form (T-like), this causes a mispairing from ~C-G to ~T-A. 2-Aminopurine is an adenine analog, pairs with thymine or cytosine. Can cause a T to C transition. Hypoxanthine arises from spontaneous deamination of adenine, pairs with cytosine. Causes an T-C transition.
Base analogs
DNA repair pathways- mech: [blank] conditions: may be used to repair UV-light induced damage, spontaneous hydrolysis/deamination, or low level alkylating agent induced damage (single base (she said 1-3 or 4 bases)) how: DNA [blank] removes the base (apurinic/apyrimidinic) AP [blank] cleaves the backbone an [blank] removes the deoxy-nucleotide (in E. coli) DNA pol I fills the gap ligase seals the nick
Base excision repair, glycosylase, endonuclease, exonuclease
mutations- [blank] modify bases - changing their base-pairing qualities. examples: [blank] (HNO2 ) causes oxidative damage exposure can cause spontaneous Deamination of cytosine and adenine (C -> U, A -> hypoxanthine) [blank] modifies cytosines (2 ways) can react to form nitrous acid can alter cytosine so that it pairs with adenine. [blank] agents modify bases by adding alkyl-groups (i.e. methyl or ethyl groups) to different positions on bases.
Chemical mutagens, Nitrous acid, Hydroxylamine, Alkylating
Protein involved in DNA replication in E. coli: [blank] Function: Unwinding DNA
DNA gyrase
Protein involved in DNA replication in E. coli: [blank] Function: Covalently links Okazaki fragments
DNA ligase
Protein involved in DNA replication in E. coli: [blank] Function: Excises RNA primer, fills in with DNA
DNA polymerase I
Protein involved in DNA replication in E. coli: [blank] Function: Elongation (DNA synthesis)
DNA polymerase III holoenzyme
DNA repair pathways- mech: [blank] by [blank] conditions: Repair (in visible light) of spontaneous base hydrolysis, chemical damage, or other forms of damage. (get ride of pyrimidine dimers) how: [2nd blank] use energy from visible light to break the covalent bonds that formed
Direct reversal, photolyases
Protein involved in DNA replication in E. coli: [blank] Function: Initiation factor; origin-binding protein
DnaA
Prokaryote DNA synthesis- Starting - [blank] binds to the Ori, which are A-T rich, and helps to melt the double helix. [blank] loads the [blank] helicase at the Ori, which moves along the open helix (in both directions) to separate the strands in coordination with DNA [blank] holoenzyme 1. DNA [blank] and [blank] unwind the double helix; SSB coats single-stranded DNA. 2. Primase ([blank]) synthesizes an RNA primer on each template strand. Each DNA pol III [blank] is attached to its template strand via the [blank] (<- subunit of pol III ->) (loaded by the [blank]). 4. The lagging strand template must loop so that the DNA polymerase machinery moves in the same direction on both strands. Completion of the synthesis of an Okazaki fragment activates [blank], which opens the [blank]. 5. The [blank] must the reload the [blank] at the [3 or 5?]' end of the next RNA [blank] on the lagging strand. 6. The DNA [blank] removes the RNA primers and replaces NMPs with dNMPs. DNA [blank] seals the nick. Stopping - Terminator sites (ter) are located [blank] to the Ori in bacterial genomes. [blank] proteins bind to ter sites and prevent continued unwinding. ter[blank], ter[blank], ter[blank] block the counterclockwise fork; ter[blank], ter[blank], ter[blank], and ter[blank] block the clockwise fork.
DnaA, DnaC, DnaB, Pol III, gyrase, DnaB, SSB, DnaG, core, b-clamp, g-complex, t, b-clamp, g-complex, b-clamp, 3, primer, pol I, ligase, opposite, Tus, A, D, E, C, B, F, G
Protein involved in DNA replication in E. coli: [blank] Function: 5' -> 3' helicase (DNA unwinding)
DnaB
Protein involved in DNA replication in E. coli: [blank] Function: DnaB chaperone; loading DnaB on DNA
DnaC
[blank] or [blank] - Addition or removal of one or more base pairs. ("indels") may be caused by errors in replication (replication [blank]) or by the formation/incorrect repair of [blank].
Insertions, deletions, slipping, double-stranded breaks,
mutations- (insertions or deletions) [blank] - planar molecule that can bind between bases of DNA. cause distortions that alter the distance between base pairs.
Intercalating agents
Eukaryote DNA synthesis- Starting - [blank] (occurs in G1) requires the assembly of pre-replication complexes at each origin of replication (late M or early G1). The [blank] binds to the origin and recruits [blank], [blank], and [blank]s (one of these proteins is a helicase - held inactive in G1). With the start of S-phase, the [blank] binds to its CDK and activates its kinase activity. S-CDK phosphorylates its targets. Phosphorylation of [blank] proteins activates the helicase and recruits [blank] and a [blank]. Phosphorylation of [blank] and [blank] recruits [blank] and DNA [blank]. Replication occurs bidirectionally (i.e. two replication forks). How prevent origins from being licenced again in S-phase: [blank] is active during S, G2, and M. It prevents [blank] proteins from binding to ORC (and blocks [blank] formation before the end of M).
Licensing, ORC (origin of replication complex), Cdc6p, Cdt1, MCM, S-cyclin, MCM, Cdc45, primase, Sld2, Sld3, Dpb11, polymerase, Geminin, MCM, preRC
DNA repair pathways- mech: [blank] conditions: single nucleotide errors (enhances replication fidelity) The DNA helix must be [blank]. When can this repair occur during the cell cycle? in coordination with [blank] how: [blank] recognizes the mismatch and recruits [blank], which feeds the DNA through the complex until it encounters a methyl group, in order to identify the parent strand. [blank] cleaves the new strand and [blank] + exonuclease removes the bad sequence. Now DNA polymerase can try again before DNA ligase seals the nick.
Mismatch repair, hemi-methylated, DNA synthesis, MutS, MutL, MutH, UvrD, UvrD
DNA repair pathways- mech: [blank] conditions: Double-stranded break repair When can this repair occur during the cell cycle? [blank] how: [blank] binds ends; recruits proteins that brings ends together DNA [blank] seals the gaps
NHEJ (Non-homologous end joining), any time, Ku70/80, ligase
DNA repair pathways- mech: [blank] conditions: may be used to repair UV-light-induced damage, major damage by alkylating agents, or other major sites of DNA damage. how: DNA [blank] removes the base (apurinic/apyrimidinic) AP [blank] cleaves the backbone an [blank] removes the deoxy-[blank] (in E. coli) DNA pol I fills the gap ligase seals the nick
Nucleotide excision repair, glycosylase, endonuclease, exonuclease, nucleotides,
Sites of potential damage to DNA: [blank] damage, Spontaneous [blank], Nonenzymatic [blank] by SAM
Oxidative, hydrolysis, methylation
In prokaryotes, b-clamp is analogous to the [blank] in eukaryotes, but has [#] subunits instead of [#].
PNCA, 2, 3
mutations- [blank] - (substitution of one base pair for another), may be caused by errors in DNA replication (rare) or by chemicals that alter the structure of a base. Arise due to rare [blank], the presence of base analogs, spontaneous hydrolysis, exposure to chemical mutagens that modify base structure
Point Mutations, tautomerization
Protein involved in DNA replication in E. coli: [blank] Function: Synthesis of RNA primer
Primase (DnaG)
In telomerase, The [blank] can hybridize with the end of the completed strand and provides a template to extend the [3 or 5?]' end of the top strand. (binds and extends many times) Then most of the bottom strand can then be synthesized by DNA [blank].
RNA template, 3, polymerase
mutations- (insertions or deletions) [blank] can also induce double stranded breaks; indels occur if this damage is not repaired precisely
Radiation damage
mutations- [blank] - base transiently changes its structure example: A-imino pairs with cytosine instead of thymine, leading to an A-T to G-C transition in the next generation.
Rare tautomerization
In prokaryotes, g-clamp is analogous to the [blank] in eukaryotes
Replication factor C (RFC)
Protein involved in DNA replication in E. coli: [blank] Function: Single-stranded DNA binding
SSB
[blank] - GC-rich repeat sequences that are gene-poor, protect the ends of linear chromosomes, replicated by the enzyme [blank] - it contains an enzyme called [blank] and an [blank] that serves as a template for replication. [3rd blank] uses [4th blank] as a template for [blank] synthesis.
Telomers, telomerase, TERT, RNA, DNA,
mutations- [blank] - a purine (or pyrimidine) is replaced by a different purine (or pyrimidine) (A <-> G, or C <-> T)
Transitions
Protein involved in DNA replication in E. coli: [blank] Function: Termination
Tus
mutations- [blank] in DNA would be highly mutagenic spontaneous [blank] of [blank] to [1st blank] or inappropriate incorporation of [1st blank] [1st blank]-DNA [blank] is responsible for excising the base corrected through base excision repair.
Uracil, deamination, cytosine, glycosylase
Subunits of E. coli DNA Polymerase III Holoenzyme: [blank] Function: Polymerase ("core" enzyme)
alpha
Which eukaryotic DNA polymerase? Nuclear; initiation of a nuclear DNA replication
alpha
Subunits of E. coli DNA Polymerase III Holoenzyme: [blank] Function: Sliding clamp processivity (holds core enzyme on template)
beta
Which eukaryotic DNA polymerase? DNA repair
beta
In eukaryotes, Progression through the cell cycle is regulated by [blank] and [blank]. [1st blank] are produced (late G1, early S) in a phase -specific manner. [1st blank] activate [2nd blank] (kinase enzymes that phosphorylate/ activate proteins) that stimulate phase - specific events
cyclins, CDKs
Which eukaryotic DNA polymerase? Nuclear; principal polymerase in lagging-strand synthesis; highly processive
delta
Subunits of E. coli DNA Polymerase III Holoenzyme: [blank] Function: 3'-Exonuclease ("core" enzyme)
epsilon
Which eukaryotic DNA polymerase? Nuclear; leading-strand synthesis, sensor of DNA damage checkpoint control
epsilon
[blank] have linear chromosomes and multiple origins of replication
eukaryotes
mutations- insertions or deletions in the coding sequence can lead to [blank] - alter the amino acid sequence or lead to a premature stop codon.
frameshift mutations
Subunits of E. coli DNA Polymerase III Holoenzyme: [blank] Function: DNA template binding; core enzyme dimerization (responsible for loading the beta-clamp onto DNA)
gamma
Which eukaryotic DNA polymerase? Mitochondria; mitochondrial DNA replication
gamma
[blank] have circular chromosomes and a single origin of replication (Ori)
prokaryotes
(UV irradiation can cause dimerization of [blank], which distorts DNA) When sequential bases of [blank] are exposed to UV radiation, it can cause formation of a [blank] ring (carbons of 2 [2nd blank] are covalently bound), causing local DNA distortion.
pyrimidines, thiamine, Cyclobutyl
Subunits of E. coli DNA Polymerase III Holoenzyme: [blank] Function: epsilon-subunit stabilization ("core" enzyme)
theta