Chapter 8 RNA

Same sequence except Thymine is now Uracil and same polarity in 5 to 3 direction.

The strand whose base sequence is identical to the base sequence of the RNA transcript produced.

The DNA template is complementary and has the opposite polarity of 3 to 5.

1

TTGACA

Most common letter at each position when comparing multiple sequences. C and G.

Multiple subunits, Beta and Beta, Alpha and Alpha, Omega and Sigma. Beta forms the catalytic center and polymerase activity. Alpha is enzyme assembly and promoter recognition. Omega is assembly. Sigma is promoter specificity.

All core and sigma, no sigma, both have affinity for DNA promoter but Holoenzyme has greater affinity for promoter DNA.

RNA polymerase will bind to DNA and sometimes the DNA will not have the promoter DNA so it hops unto another strand until it finds one with the promoter necessary for RNA transcription to begin. It disassociates and associates till.

Affinity and how well something binds to one another

The sigma subunit apart of the holoenzyme prevents it from going too far from the DNA promoter and pauses the RNA polymerase. The Holoenzyme must become a core to continue without so the sigma disassociates and reassociates once RNA polymerase moves forward.

Holoenzyme

TATAAT

Core enzyme

Hairpin and Rut (Rho-utilization) site, Hairpin causes RNA polymerase to pause, it is tugging. Rho catches up and unwinds RNA from the RNA polymerase.

Rho is a homohexamer that makes a ring around the mRNA and has helicase function. Moves 5-3 along mRNA.

Endonuclease and it can be blocked by ribosomes. Products from RNase E will be degraded by 3 end exonuclease.

mRNA is single stranded and wants to base pair so it does with itself.

Regulates a hairpin immediately followed by a run of U's. RNA polymerase pauses because hairpin formation applies tension. A/U base pairs cannot hold RNA on and disassociates from DNA.

Hairpin and Rho-utilization site. Rho is a homohexamer that makes a ring around the mRNA and has helicase function. Moves along 5-3 mRNA. Hairpin causes RNA polymerase to pause and allows the Rho to catch up and unwind RNA from RNA polymerase.

2 minutes

Endonuclease that breaks down RNA strand and is blocked by ribosomes.

RNase E will bind to a monphosphate 5 end after pyrophosphohydrase cleaves a pyrophosphate grouops.

Half life will also increase for RNA strand.

mRNA, tRNA, rRNA

Acceptor arm, Pseudoridine arm, Variable arm, Anticodon arm, D arm

Scaffold and Enzymatic activity at catalytic site

specific amino acid + specific uncharged tRNA = t tRNA-AA charged

Scaffold and Enzymatic activity and catalytic site

Large 50s subunit and small 30s subunit, Large 60s subunit and small 40s subunit.

70s in prokaryotes and 80s in eukaryotes

Large subunit rRNA forms the catalytic site for peptide bond formation, small subunit has rRNA sequences that base pair with shine Delgarno sequence.

It makes sure the start codon is in the p site and helps with basepairing of small subunit.

E site is the exit site, A site is bound by the aminoacyl tRNA, P site is bound by the peptidyl tRNA.

An exit tunnel allowing the growing polypeptide to exit.

Initiation factor 3 binds the small subunit and prevents association with large subunit. Blocks E site.
Initiation factor 1 blocks A site.
Initiation factor 2 a G protein with GTPase activity, binds GTP then initiation tRNA to form a ternary complex.

It is made of the IF2, GTP and initiation tRNA. It binds to the small subunit and places the initiation tRNA in the P-site.

GTP a energy source equal to ATP

A monomeric G protein that brings aminoacyl tRNA to the A site of the ribosome. Remains bound to GDP. codon/anti-codon recognition causes a conformational change in the ribosome which stimulates the GTPase activity of EF-Tu. The energy released by GTP hydrolysis activates the peptidyl transferase activity of the ribosome to form a peptide bond between the carboxy terminus of the polypeptide (attached to the tRNA in the P-site) and the amino group of the amino acid (attached to the tRNA in the A-site); also causes EF-Tu-GDP to dissociate.

GTPase activating protein, Guanine Nucleotide Exchange Factor

EF-G is a G protein that will bind near A site and cause a shift from newly formed peptide bond to p site and uncharged trna into e site

A guanidine exchange factor exchanges the GDP bound to EF-Tu for GTP thereby reactivating the EF-Tu allowing it to bind another tRNA and repeat the process.

Release factors (RFs, Class 1 and 2) and ribosome recycling factors

Stop; Charged tRNAs

RF1 is a release factor that binds to the UAA or UAG stop codon in the A site. RF2 is a release factor that binds to the UAA or UGA stop codon in the A site.

The class II RF (RF3) is a G protein that binds RF1/2; GTP hydrolysis causes dissociation of the RFs from the ribosome.

1) a peptide anticodon that matches the stop codon and 2) a GGQ (glycine, glycine, glutamine) domain that goes into the peptidyl transferase active site where the glutamine residue coordinates a water molecule for hydrolysis of the bond between the last AA of the new polypeptide and the peptidyl tRNA.

The ribosome recycling factor binds to the A site, followed by the association of the EF-G/GTP with the ribosome. EFG hydrolyzes GTP and changes conformation pushing the RRF to the P site and disassociating ribosome/mRNA/—uncharged tRNA.