Proteins and DNA Flashcards
What are the steps in replication in an E. coli replication fork?
1) Topoisomerase removes superhelicity
2) ori forms
3) Helicase unwinds fork
4) Single strand binding (ssb) protein coats to prevent reassociation
5) RNA pol/primase adds RNA primer
6) DNA pol-III synthesizes leading strand, displacing ssb protein
7) Lagging strand filled-in short segments by pol-I leaving “gaps”
8) DNA ligase seals single strand breaks
What enzyme is responsible for DNA repair?
DNA polymerase
What enzyme seals single strand breaks?
DNA ligase
What enzyme removes superhelicity?
Topoisomerase
What enzyme unwinds replication fork?
Helicase
What protein is responsible for preventing re-association of the two DNA strands during replication?
Single strand binding protein
What is the function of DNA pol-III during replication?
Synthesizes leading strand, displacing single strand binding protein
What enzyme fills in the lagging strand during DNA replication? What seals the gaps that it leaves behind?
Pol-I but it still leaves gaps, which are sealed by ligase
What is transcription and what catalyzes it?
- Synthesis of mRNA complementary to DNA
- Catalyzed by RNA polymerase III
Where does RNA polymerase bind DNA? What sequence is required? What are the base patterns called?
- RNA polymerase binds DNA at special regions termed “promotors”
- Base patterns called consensus sequence
- 7 base “TATA” or “Pribnow” box aligns RNA polymerase docking
- The -35 sequence is the initial site of RNA polymerase binding (35 bases “upstream” from mRNA start)
What are the initiation steps in mRNA synthesis?
1) Polymerase binds promotor sequence in duplex DNA “closed complex”
2) Polymerase melts duplex DNA near transcription start site, forming transcription bubble “open bubble”
3) Polymerase catalyzes phosphodiester linkage of two initial rNTPs
What is the elongation step in mRNA synthesis?
4) Polymerase advances 3’-5’ down template strand, melting duplex DNA and adding rNTPs to growing RNA
- DNA = 3’ - 5’
- RNA = 5’ - 3’
What is the termination step in mRNA synthesis?
5) At transcription stop site, polymerase releases completed RNA and dissociates from DNA
What are some RNA post-transcriptional modifications?
- Primary transcript is modified in the nucleus:
- 5’ capping (7-methyl guanosine) (stops it from being degraded)
- 3’ polyadenylation (poly A)
- RNA splicing (removal of intron sequences - intervening base pairs in coding sequences of DNA that do not directly code for genes)
- Isoforms and alternative splicing
In transcription, what is the difference between “sense” and “antisense” strands?
- “Sense” strands directly code for amino acids (mRNA strand is sense, non-template strand in DNA is sense)
- “Antisense” strands are template strands (read from 3’ to 5’) - copied by RNA polymerase to RNA strand)
