C3 of one nucleotide linked to C5 carbon of next nucleotide via Pi

1) DNA binding proteins fit into major and minor grooves and recognize bases by forming what?

2) What fits in the major groove?

1) non-covalent bonds w/bases in groove

2) alpha helixes fit in major groove

1) Linker histone H1 helps do what?

2) Histone modification will be important in what?

1) fold nucleosomes into higher structures to form chromasome

2) important in gene regulation as compact DNA structures can't be transcribed into RNA

1) How many origins of replicaton do bacteria genomes have?

2) What happens at the ori?

3) How many replication forks?

4) Do eukaryotes have same number of ORi?

1) 1

2) this is where dbl helix melts and semi-conservative DNA replication begins

3) ORI has 2 replication forks, one at each end

4) NO eukaryotes have more than one

1) Where does DNA syn begin?

2) What unwinds the DNA double helix, what provides the energy?

3) What keeps the DNA from reannealing?

4) What way does the replication for move?

1) replication fork

2) DNA helicases hydolyzing ATP

3) single strand binding proteins

4) replication fork moves away from Ori so "bubble" around Ori lengthens

1) What supercoils are natural in circular or constrained B-form DNA

2) What allows supercoiling to relax?

1) negative

2) nicking=breaking of one of the two DNA single strands

1) what does topoisomerase 1 do? Does it require ATP?

2) Type II topoisomerase works how? Does it require ATP?

1) Type I creat transient single stranded break in DNA

2) Type II transiently breaks double stranded breaks in DNA

1) DNA polymerase catalyzes syn in which direction?

2) DNA poly moves along template strand in which direction?

1) syn 5' to 3'

2) moves 3' to 5'

1) How does DNA syn occur?

2) what kind of bond is formed?

3) is this reversible, why or why not?

1) occurs 5' to 3'. 3' OH of one nucleotide attacks 5' phosphate of incoming nucleotide

2) forms 5' to 3' phosphodiester bond

3) IRREVERSIBLE b/c PPi

1) Can DNA polymerase initiate syn of primer de novo?

2) what enzyme is required to generate primer?

3) What primer is syn that is used for extension by DNA polym?

1) no

2) primase

3) RNA primer which provides 3' OH for extension

1) What is the easy template?

2) what is the difficult template?

1) leading strand

2) lagging strand

1) 5' to 3' direction of DNA syn means that both strands of DNA syn at the replication fork are?

2) On the leading strand, DNA primase creates what?

3) on the lagging strand, several primers are created for what?

1) means that DNA syn at repl fork are NOT identical

2) 1 primer for continuous replication

3) discontinous syn of several Okazaki fragments

1) 5' to 3' poly activity-incorp dNTPs into growing chain

2) 5' to 3' exonuclease activity-remove RNA primers on lagging strand

3) 3' to 5' exonuclease activity-proofreads newly syn strand

Replication fork: leading strand

1) to make lagging strand continous the RNA primers are degraded via what?

2) how does it work?

1) 5' to 3' exonuclease act of DNA pol

2) removes ribonucleotides from 5' end of Okazaki fragment

Replic Fork: Leading strand

3) 5' to 3' polymerase activity of another DNA poly then fills the resultant gaps with DNA and what joins the tow fragments?

4) DNA ligase seals broken phosphodiester bonds by what/using what?

3) DNA ligase

4) activating 5' end w/ATP and then coupling ATP hydrolysis to form new phosphodiester bond

1) what is the problem seen in eukaryotes that DNA poly can't do?

2) why is this?

3) What fills the gap b/c there is no 3' OH to extend from?

1) extend the extreme 5' end of the lagging strand

2) RNA primer runs out of room for last Okazaki fragment

3) telomeres-tandem repeats of G-rich sequences

1) telomers are syn by?

2) Telomerase is RNA-protein complex that is a?

3) how does telomerase RNA work?

4) what is formed?

1) telomerase

2) reverse transcriptase-can syn DNA from RNA template

3) telomerase RNA is complementary to G-rich repeat at the telomeres and base pairs with it

4) once base pairs forms a primer template for elongation of the 3' end of telomere and then completed by DNA polymerase

protective mechanism to prevent uncontrolled cell proliferation of abnormal cells

"cancer cells have increased telomerase activity"

1) hydrolytic attack

2) oxidative damage

3) uncontrolled methylation

what is oxidative deamination?

what does this lead to?

NH2 is replaced w/dbl bond O

unnatural DNA bases-adenine to hypoxanthine so instead of A-U base pair you get H-C

ex. C to U most common

glycosidic bond btwn purine bases and sugar in a nucleotide spon hydrolyze leaving APURINIC SUGAR

"depurination repaird directly by AP endonuclease"

What kind of DNA damage can be induced by UV radiation?

pyrimidine dimer-adjacent thymines linked via a cyclobutane ring

blocks replication and transcription

what is base-excision repair?

what recognizes and cleaves bond btwn base and deoxyribose?

what is this damaged bas called?

What removes sugar-phosphate backbone leaving gap

what fills and seals gap

single damaged base

DNA glycoslase

Apurinic or apyrimidinic site

AP endonuclease

DNA polym and DNA ligase

Nucleotide excision repair is what?

what are the steps

NER repairs bulky adducts (thymine dimers) and damage not recognized by DNA glycosylases

Steps:

1) multienzyme complex scans DNA dbl helix

2) NUCLEASE cleaves phosph backbone on both sides

3) helicase unwinds area w/lesion

4) gap is repair by DNA poly and DNA ligase

What is mismatch repair?

What scans the DNA and selectively binds to mismatched base?

Is the mismatched nucleotide removed from the newly syn strand?

What protein scans nearby DNA for a nick and degrades DNA from nick to mismatch?

Are nicks confined to new strands in eukaryotes?

Mismatch repair repairs base-pair mismatches that are missed by proofreading sys

MutS protein

yes only the newly syn strand="strand directed"

MutL

yes

What causes dbl stranded breaks?

Is there a template strand for repair?

What is the most effective way of repairing dbl stranded breaks?

What restores complete sequence by copying the second chromosome?

ionizing radiation, oxidizing agents, metabolic cell producs, replication errors

no

nonhomologous end joining=cause loss of one or more nucleotides

homologous end joing=recombination

Initiation of transcription in bacteria

1) Is bacterial RNA poly a multi-subunit complex?

2) bRNA poly requires this detachable thing to initiate transcription?

3) Holoenzyme slides along DNA until it encounters what?

4) Binding of the RNA poly to the promoter does what to the double helix?

5) What does RNA polym do then?

1) multi-subunit complex

2) sigma factor

3) a promoter sequence w/specific contact

4) opens it up

5) slowly adds rNTPs then RNA poly undergoes conformational change releasing sigma factor

it is transcribed into RNA and the RNA then forms hairpin which stops RNA poly and it dissociates

"once dissociated it rebinds w/sigma forming holoenzyme"

Where does transcription begin in prokaryotes?

Eukaryotic transcription intitiation

What is the main DNA sequence that signals transcription intitiation?

What is it similar to in bacterial promoters?

When are these sequences seen?

TATA box 25 nts upstream that is recognized by TBP (CAAT box recognized by CTF)

similar to -10 (pribnow box)

in ALL genes transcribed by RNA poly II and recognized by general transcription factors

TFIID binds what in Eukaryotic initiation?

TFIIH contains what activity and does what?

TFIID binds 1st via the TBP subunit w/TATA box

TFIIH contains helicase activity to unwind DNA & also is a kinase that phosphorylates RNA poly

What initiates elongation in eukaryotes?

What does elongation induce?

kinase phoshporylating the RNA polym causing conformational change so it releases itself

supercoiling

RNA polymerase carries what protein on its C-terminal tail that is transferred to mRNA at the appropriate time?

When does RNA processing protein bind?

When is trasfer of protein to nascent mRNA occur?

When does RNA polym become dephosphorylated on its tail?

pre-mRNA processing protein

bind to poly tail when phosphorylated towards end of initiation phase

during elongation

once its completed transcription so that it can reinitiate

RNA processing

RNase P cleaves the tRNA 5' end, UU at the 3' end is replaced by what?

What does this change?

UU at the 3' end is replaced w/ CCA

changes H-bonding patterns

5' cap, poly A tail added to 3'end and introns spliced out

**not all sequences in mRNA are translated into protein

What is the structure of the 5' cap?

What is its role in mRNA's?

m7G==7 methyl guanosine

its role is to stabilize the mRNA molecule and binds a CBC protein to aid in export of mRNA to cytosol

also helps align mRNA on ribosome during translation

Overall RNA splicing reaction

The reaction involve what kind of reaciton?

Splicing is carried out by snRNAs bound to form snRNPs that do what?

What do snRNPs assemble into?

Where does spliceosome recognize splicing signals?

recognize the splice sites and facilitate catalysis

spliceosome-lrg complex that performs RNA splicing

pre-mRNA

what is the branch point sequence is splicing mechanism?

How is RNA lariat formed?

A where snRNPs bind near 3' end

RNA lariat is formed from 5' cleavage and then the 3' end is cleaved removing the intron

what is polyadenylation?

What happens after syn/addition of poly A tail?

What keeps poly A single?

What is the role of poly A tail?

3' end of eukaryotic mRNA are modified by addition of tail that contains several hundred A bases

processing proteins bind

poly A binding proteins

help stabilize mature mRNA

Rifampin binds to prokaryotic RNA poly but NOT eukaryotic versions

BACTERIAL GROWTH SLOWS w/out interfering w/ RNA syn in pateint

What does export ready mRNA mean?

What does it have to have?

export ready mRNA is capable to go from nucleus to cytoplasm **selective**

1-CAP binding complex

2-RNA export factors

3-snRNPs absent