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126 terms

CH. 28, 29 notes/book

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features of Watson-Crick model. 1. 2 polynucleotide chains running in opposite directions coil around a common axis to form a __-handed double helix
purine, pyrimidine, phosphate, deoxyribose
features of Watson-Crick model. 2. __ and __ bases are on the inside of the helix, whereas ___ and __ are on the outside.
thymine, cytosine, 2, 3
features of Watson-Crick model. 3. adenine is paired w/__, and guanine w/__. an a-t- base pair is held together by __ H bonds, G-C base pair is held together by __ bonds.
wider, shorter, tilted base pairs
what is the A helix like compared to the B helix?
hydroxyl, phosphate
Review DNA Structure: antiparallel strands
3' ___, 5' ___
3, 2
A form DNA Ribose is C-_' endo, B form DNA RIbose is C-__' endo
B form
which form of DNA is found most often in vivo?
A
which form? A or B is dehydrated?
glycosidic bonds are not diametrically opposite to one another
why do major/minor grooves form?
wider (12 A), deeper (8.5 A)
2 qualities of major groove in relation to minor groove? B form
thymine
the methyl group of what lies in the major groove?
N-3, O-2, C-2
Minor Groove
H bond acceptors
__of Adenine or Guanine
__ of Cytosine or Thymine
H bond donors
Amino __ of G
N-7, O-4, C-6, C-4
Major Groove
H bond acceptors
__ of G or A
__ of T
H bond donors
Amino groups of ___ of A or __ or C
left-handed, phosphates zigzagged
what is the major difference between the z DNA and regular DNA? how does it get its name?
linking number
__ __: equal to the # of times a strand of DNA winds in the right handed direction around the helix axis when the axis is constrained to lie in a plane.
topological isomers, topoisomers
mlcls differing only in linking # are ___ __ or ___.
twist
__ is a measure of the helical winding of the DNA strands around each other
writhe
__ is a measure of the coiling of the axis of the double helix. (supercoiling)
-, +
a right handed coil has +/- supercoiling while a left handed coil has +/- supercoiling.
Lk
the sum of Tw and Wr is = to what?
type 1
__ ___ topoisomerases catalyze the relaxation of supercoiled DNA.
type 2
__ __ topoisomerases utilize free energy from atp hydrolysis to add - supercoils to DNA
cleavage, passage, resealing
3 stage process of topoisomerases
tyrosine
the 2 types of topoisomerases use __ residues to form covalent links to the polynucleotide backbone that is transiently broken.
4, 20
human type 1 topoisomerase comprises __ domains, which are arranged around a central cavity having a diameter of __A. DNA binds inside cavity. Nucleophilic attack on phosphate by hydroxyl tyr 723: Release of free 5' hydroxyl; Covalent intermediate with phosphate. Rotation around intact DNA strand: Energy from supercoiling, Free hydroxyl of DNA attacks the phosphotyrosine residue: Tyr released .
type 2
which type of topoisomerase doesn't allow the DNA to rotate?
novobiocin
___(drug) blocks the binding of ATP to gyrase.
nalidixic acid, ciprofloxacin
__ __ and __ interfere with the breakage and rejoining of DNA chains. these 2 gyrase inhibitors are widely used to treat urinary tract & other infections inc those due to bacillus anthracis.
camptothecin
__ an antitumor agent, inhibits human topoisomerase 1 by stabilizing the form of the enzyme covalently linked to DNA
DNA polymerases
__ __ are template-directed enzymes
metal ions
DNA polymerases req __ __ for activity.
aspartate
the 2 metal ions are bridged by the carboxylate groups of 2 ___ residues in the palm domain of the polymerase.
yes
can primase initiate synthesis w/out a primer?
replication fork
the site of DNA synthesis is called the __ __ bc the complex formed by the newly synthesized daughter helices arising from the parental duplex resembles what its name is.
lagging, leading
the strand formed from okazaki fragments is considered the __ strand, while the other one is the __ strand.
DNA ligase
this enzyme catalyzes the formation of a phosphodiester bond btwn the 3' hydroxyl group at the end of 1 dna chain and the 5' phosphate at the end of the other.
ATP, NAD+
for dna ligation, an energy source is required. in eukaryotes and archaea, the source is __, in bacteria, it is __.
no
does ligase link 2 mlcls of single-stranded DNA or circularize single-stranded DNA?
helicases
specific enzymes, ___, utilize the energy of ATP hydrolysis to power strand separation (unwinds helix), binds near origin and / or replication fork
A2, B2
Four domains in bacterial helicase : PcrA comprises 4 domains. A1, A2, B1, B2. which 2 have unique structures?
A1
PcrA comprises 4 domains. which domain contains a P-loop NTPase fold and participates in ATP binding and hydrolysis?
B1
PcrA comprises 4 domains. which domain is homologous to A1 but lacks a P-loop?
A1, B1, DNA
which PcrA domains are capable of binding single-stranded DNA? in the absence of bound ATP, both domains are bound to __. the binding of ATP triggers conformational changes in the P loop and adjacent regions that lead to the closure of the cleft btwn these domains.
4.6
the e coli genome cntns __ million bp and is copied in less than 40 mins.
processivity
__ refers to the ability of an enzyme to catalyze many consecutive rxns w/out releasing its substrate. (# of nucleotides incorporated for each association of enzyme with the template / primer.)
B2
the __ subunit of DNA poly 3 plays a key role in replication by serving as a sliding DNA clamp.
245
the ecoli oriC is a ___ bp region.
5
the oriC locus cntns __ copies of a seq that are preferred binding sites for the origin-recognition protein DnaA
13, AT
the oriC locus cntns a tandem array of __ bp sequences that are rich in __ base pairs.
binding of DnaA proteins to DNA
what is the 1st step in the preparation of DNA for replication?
AAA
DnaA is a member of the Ploop NTPase family and more spec, an ___ ATPase. each DnaA monomer comprises an ATPase domain linked to a DNA-binding domain at its c terminus. DnaA mlcls are able to bind to each other through their ATPase domains.
30,000, replicon
in human beings, replication requires about __ origins of replication. each origin of replication is the starting site for a replication unit, or ___.
circular
what is the shape of the genomes (ori c) of prokaryotes?
linear
what is the shape of the genomes (ori c) of eukaryotes?
telomerase
__ is a specialized reverse transcriptase that carries its own template. __ is gen. expressed @ high levels only in rapidly growing cells.
huntington disease
__ __, an autosomal dominant disease expresses a protein in the brain which contains a stretch of consecutive glutamine residues. these residues are encoded by a tandem array of CAG seq w/in the gene.
anticipation
in huntington disease, the unaffected persons have an array btwn 6-31 repeats. in affected it is 36 and 82 repeats or longer. the array tends to become longer from generation to generation. the consequence is a phenomenon known as ___.
oxidation, deamination, alkylation, radiation, UV rays
what 5 processes can alter specific bases w/in DNA after replication is complete?
MutS, MutL, MutH
in e coli, the proteins that are used to detect the mismatch of replication and recruiting an endonuclease to cleave the newly synthesized dna are what? the endonuclease is what?
direct repair
an ex of __ __ is the photochemical cleavage of pyrimidine dimers. nearly all cells cntn a photoreactivating enzyme called DNA photolyase.
base excision repair, glycolyase, ap site
the excision of modified bases such as 3-methyladenine by the E coli enzyme AlkA is an ex of __ __ __. the binding of this enzyme to damaged DNA flips the affected base out of the DNA double helix & into the active site of the enzyme. The enzyme then acts as a __, cleaving the glycosidic bond to rls the damaged base. the DNA backbone is intact but a base is missing. this hole is called an __ __. an AP endonucleases recognizes this defect and nicks the backbone adjacent to the missing base. deoxyribose phosphodiesterase excises the residual deoxyribose phosphate unit and the dna polymerase 1 inserts an undamaged nucleotide. finally the repaired strand is sealed.
to enhance the fidelity of the genetic message
thymine is used in dna instead of uracil why?
initiation, elongation, termination
3 stages of RNA synthesis?
promoter sites, promoters, cis-acting elements
RNA polymerase: 1. It searches DNA for initiation sites, also called __ __ or simply __. Bc the seq are on the same mlcl of DNA as the genes being transcribed, they are called __ __ __. 2. it unwinds a short stretch of dbl-helical DNA to produce a single-stranded DNA template from which it takes instructions.
alpha2 beta beta' sigma
the holoenzyme of e coli (prokaryotic) rna polymerase is __ __ __ __
sigma
the __ subunit helps find a promoter site where transcription begins, participates in the initiation of rna synthesis, and then dissociates from the rest of the enzyme.
alpha2 beta beta'
the core enzyme of e coli rna polymerase which contains the core enzyme is what?
promoters
__ are sequences of DNA that direct the rna polymerase to the proper initiation site for transcription.
-10, -35, core promoter
2 common motifs are present on the 5' (upstream) side of the transcription start site. known as what? the region cntng these seq is called the __ __.
sense strand, antisense strand
the coding strand is also known as the __ __ and the temp strand as the __ __.
sigma32
e coli responds by synthesizing __ which recognizes the promoters of heat-shock genes.
sigma
__ plays a key role in determng where RNA polymerase init transcription.
yes
can RNA synthesis start w/out a promoter?
pppG, pppA
most newly synthesized RNA chains carry a highly distinctive tag on the 5' end: the 1st base @ that end is either ___ or ___
accessory proteins
RNA polymerases do show proofreading nuclease activity, particularly in the presence of __ __.
GC, AT
the transcribed regions of DNA templates cntn stop signals. the simplest one is a palindromic __ rich region followed by an __rich region. the RNA transcript of this DNA palindrome is self-complementary
hairpin, U
RNA polymerase needs no help to terminate transcription at a ___ followed by sev __ residues. at other sites, termination req the part of an addtl factor.
ATP synthase
hexameric rho, which is structurally similar & homologous to __ __ specifically binds single stranded rna. (w/the single stranded rna playing the role of the gamma subunit)
rifampicin
__ does not block the binding of rna polymerase to the dna template, rather it interferes with the formation of the first few phosphodiester bonds in the rna chain. it blocks the channel into which the rna-dna hybrid generated by the enzyme must pass. binding site is 12 A from the active site itself. can be used in antituberculosis therapy
actinomycin D
__ __, a polypeptide-cntng antibiotic from a diff strain inhibits transcription by binding tightly and specifically to dbl helical dna and prevents it from being an effective template for rna synthesis. effective in treatment in some cancers
ribonuclease P
__ __ generates the correct 5' terminus of all tRNA mlcls in E coli.
Ribonuclease 3
_____ __ excises 5s, 16s, 23s rRNA precursors from the primary transcript by cleaving dbl helical hairpin regions at spec sites.
nuclear membrane, complex transcriptional regulation, RNA processing
eukaryotes: gene expression is influenced by 3 important characteristics unique to eukaryotes: what are they?
f (different compartments)
in eukaryotes, transcription and translation take place in the same cell compartment, t/f?
nucleus, cytoplasm
eukaryotes: transcription takes place where in eukaryotes? translation?
-10, -35, UP
what are the 3 promoter elements found in prokaryotes?
18s, 5.8s, 28s, 3, 2
eukaryotes: in prokaryotes, RNA is synthesized by a single kind of polymerase. the nucleus of a eukaryote cntns 3 types of RNA polymerase. RNA polymerase 1 is located in the nucleoli where it transcribes the tandem array of genes for __, __, and __ ribosomal RNA. the other ribosomal RNA mlcl (5S rRNA) and all the transfer RNA mlcls are synthesized by RNA polymerase __, which is located in the nucleoplasm rather than in nucleoli. RNA polymerase __, which is also located in the nucleoplasm, synthesizes the precursors of messenger RNA as well as several small RNA mlcls, such as those of the splicing apparatus.
alpha amanitin
eukaryotes: __ ___ is a cyclic octapeptide that contains several modified amino acids. Poison from mushroom, Amanita phalloides, inhibits RNA polymerase II
carboxyl terminal domain, serine
eukaryotes: although all eukaryotic RNA polymerases are homologous to one another and to prokaryotic RNA polymerase, RNA polymerase 2 contains a unique __ __ __ on the 220-kd subunit called the CTD. this domain is unusual bc it contains multiple repeats of a YSPTSPS. the activity of RNA polymerase 2 is regulated by phosphorylation mainly on the __ residues of the carboxyl-terminal domain.
RNA polymerase 3
eukaryotes: promoters for which eukaryotic RNA polymerase are within the transcribed sequence?
TATA box
eukaryotes: the most commonly recognized cis-acting element for genes transcribed by RNA polymerase 2 is called the __ __ on the basis of its consensus sequence. it is usu centered btwn positions -30, -100
initiator element
eukaryotes: the TATA box is often paired with an ___ ___, a seq found at the transcriptional start site, btwn positions -3, +5. this seq defines the start site, bc the promoter elements are at variable distances frmo that site.
downstream core promoter element
eukaryotic: a third element, the __ __ __ __, is commonly found in conjunction w/the inr in transcripts that lack the tata box. in contrast w/the tata box, it is found downstream of the stat site, btwn positions +28, +32
CAAT box, GC box
eukaryotic: addtl regulatory segments are located btwn -40, -150. many promoters contain a __ __, and some cntn a __ __.
TF2
eukaryotes: RNA polymerase is guided to the start site by a set of transcription factors known collectively as __.
TF2D
eukaryotes: initiation begins with binding of __ to the TATA box
TATA box binding protein
eukaryotes: in TATA box promoters, the key initial event is the recognition of the TATA box by the __ __ __ __, a 30 kd component of the 700 kd complex.
response elements
heat shock transcription factor differs from sigma32, a heat-shock protein of E coli in binding directly to __ __ in heat shock promoters rather than first becoming assoc w/rna polymerase
phosphatases, nucleases
Caps contribute to the stability of mRNAs by protecting their 5' ends from __ and __.
poly A
most eukaryotic mRNAs contain a ___ tail at the 3'end, added after transcription has ended.
poly A polymerase
after cleavage of the pre-RNA by the endonuclease, a __ ___ adds about 250 residues to the 3' end of the transcript, ATP is the donor in this rxn.
RNA editing
__ __ is the term for a change in the nucleotide seq of RNA after transcription by processes other than RNA splicing.
apolipoprotein B
__ __ plays an imp role in the transport of triacylglycerols and cholesterol by forming an amphipathic spherical shell around the lipids carried in lipoprotein particles.
synthesis, G2, mitosis, G1
order of the cell cycle?
DnaA, SSB, helicase, topology
Replication Fork: Formed by unwinding helix, moves bidirectionally from origin as synthesis occurs, Initiated by Pre-priming complex (what are the components of this), control of __ by topoisomerase, Synthesis, Primase, DNA Polymerase, Exonucleases, unwinding creates strain on region just beyond replication fork
origin, replication
DnaA protein binds to and melts __ of __. 20 to 50 copies / origin, origin is AT rich, low tm
DNA polymerase, nuclease
Single Stranded DNA Binding Proteins: Helix stabilizing protein, structural protein, cooperatively binds single stranded DNA (prevents reannealing of complementary base pairs: allows __ __ to read bases), (protects single stranded regions: resists
__ digestion)
agarose gel, unwinding
Amount of supercoiling affects rate of migration through an __ __ (Supercoiled faster, Open circular slower). Negative supercoiling prepares DNA for ___.
iranotecan, topotecan
Camptothecin derivatives: 2, what are they? FDA approved for treatment of colorectal and ovarian cancer
ATP, 2, gate, transported
Topoisomerase II: Relaxes or supercoils DNA by breaking phosphodiester bonds on BOTH strands of the double helix, __ req for supercoiling, Contains __ cavities for binding DNA, which segments are found on it?
Etoposide, coumarin, quinolones
Drugs that inhibit Topoisomerase II: anticancer ____, antibiotics: ___ (e.g. Novobiocin), ___ (e.g. Ciprofolaxin) inhibit gyrase
5' to 3', 3' to 5', pyrophosphate
Class of enzymes that synthesizes DNA by addition of nucleotides in a template directed fashion.
synthesis is ___
template read __
3' hydroxyl serves as a nucleophile to attack alpha phosphate of dNTP, __ = leaving group
Pol 2, pol 1, pol 3
dna polymerase: ___ Repair, __ Repair / gap filling, __ Replication
template DNA, 3' hydroxyl, dNTP's, divalent cation
4 things DNA polymerases require?
replication, repair, sliding clamp
Processivity which process is high, which is low/interm? Increased by __ __
transition
pyrimidine subs for pyrimidine OR purine subs for purine is called what?
transversion
pyrimidine replaces purine OR purine replaces pyrimidine is called what?
eukaryotes
Small Nuclear RNA (snRNA) are found in __ only.
DNA template, ribonucleoside triphosphates, divalent cation
RNA Polymerase req what 3 things?
AT
in contrast w/e coli the origins of replication in human beings do not cntn regions of sharply defined sequence. instead, more broadly defined __ rich sequences are the sites around which the origin of replication complexes (ORC) are assembled.
origin, replication complex
euk: the assembly of the __ of __ __ is the first step in the preparation for replication. is composed of 6 proteins each homologous to dnaa.
Cdc6, Cdt1, Mcm2-7
euk: after the orc has been assembled addtl proteins are recruited including __ a homolog of the orc subunits and ___. these in turn recruit a hexameric helicase w/6 distinct subunits called ___. these proteins are called licensing factors bc they permit the formation of the initiation complex. parental dna strands are separated and the single strands are stbailized by the binding of replication protein a.
initiation, elongation
phosphorylation of the carboxyl terminal domain by tf2h marks the transition from __ to __.
GU, AG
in eukaryotes, the intron begins w/ __ and ends w/__.
in mammalian cells, splicing begins w/the recognition of the ___ __ __ by the U1 snRNP.
5' splice site
2 features of the splicing process are notweorthy: 1) __ mlcls play key roles in directing the alignment of splice sites and in carrying out catalysis. 2) ATP powered __ unwind RNA duplex intermediates that facilitate catalysis and induce the rls of snRNPs from the mRNA
RNA, helicases