Prokaryotic transcription and translation - Part 2

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Explain the term 'closed complex' with reference to prokaryotic transcription
When the sigma factors bind to DNA, they are still double stranded.
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How does it become and open complex?
The B' pincer closes around the DNA and forms a channel and an active site. DNA strands separate without needed additional helicases
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Where is the double helix opened, relative to transcription start?
-11 to +3
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What is often called the transcription bubble?
The RNS Polymerase promotor open complex
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What needs to happen before the exposed bases are copied onto an RNA compliment?
Transient unwinding of dna
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When does the sigma factor dissociate from the RNAP
Once a growing 12nt transcript has moved it's sigma 3.2 loop aside.
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What do protiens GreA and GreB in elongations
act to remove any blockages arising
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What gets released when the chain is extended?
A pyrophosphate
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Two forms of termination that have been recognised
Factor dependant and factor independent termination
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What's something both types need?
The newly transcribed mRNA to promote termination, so RNA polymerase must trascribe a terminator region
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Describe factor independent termination
- inverted repeat sequence, -rich in GC bonds, -often followed by a poly U tail in the RNA, Provides a steric mechanism for the pausing and dissociation of the RNA pol.
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Describe factor dependant termination - the three factors
Tau, NusA, Rho. Little is known about them but Rho is thought to bind to a Rho Utilising site and cause dissociation through ATP hydrolysis
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Where is the control of gene expression in prokaryotes?
At the level of transcription- little separation between transcription and translation
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What are operons?
A cluster of coordinately regulated genes transcribed from the same promotor.
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Three things an operon contains
Structural genes, eg, encoding enzynes. Regulator genes, and regulatory sites
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Two other forms of RNA in the bacterial cell
transfer RNA and Ribosomal RNA
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What is transfer RNA?
The adaptor molecule that allows the genetic code to be translated into an amino acid sequence. Anti-codon and specific amino acid.
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Structure of a tRNA?
Short - between 73 and 93 nucleotides in length - and have regions of secondary and tertiary structure.
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Name the 5 areas of the tRNA
Acceptor arm, TwC loop with unusual bases, variable loop, anticodon, D loop.
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Where is the tRNA attachement site of amino acids
the 3' end where there is a conserved CCA sequence
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What is the enzyme that adds the amino acid?
aminoacyl-tRNA synthetase.
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How does aminoacyl-tRNA stop the wrong amino acid being encorporated
it has the ability to check the correct one has been added- for example serine and theronine
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How many ribosomes does E.coli have?
between 3,000 and 2,000 - highly regulated
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Describe the structure of a bacterial ribosome
a 70s ribosome, made of 50s and 30s, which themselves are made up of RNA and protiens.
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What part of the ribosome joins new amino acids onto the growing chain?
23S rRNA molecule - part of the 50s subunit.
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Translation initiation - what does the preinitation complex consist of?
30S subunit, the mRNA, formylmethionine tRNA, Initiation factors 1-3 and GTP
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What does the formylmethionine tRNA bind to?
The initation codon = AUG.
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What is the shine-dalgamo sequence? What is it for?
A stretch of 3-10 nucleotides at the 5' end of the mRNA. It is complimentary to the 16S rRNA of the 30s subunit, so the ribosome binds and is positioned at the correct start site
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Three important sites on the 30S subunit
A - aminoacyl, P - Peptidyl, and E - exit.
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What is the A site for? How is it used in initiation?
The A site on the ribosome is where each new aminoacyl-tRNA binds. In initiation - fMET tRNA binds to the P site with IF1, so the A site is blocked.
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What does IF2 do?
Starts off bound to the P-site, when IF1 is released it helps the 50s subunit to be added. When it is released the full 70s ribosome is formed - gtp hydrolysis
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What assists the attaching of new AA-tRNA at the A site?
EF-TU, elongation factor thermo unstable.
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What direction does the polypeptide grow?
Amino to carboxyl direction
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What catalyses the translocation of tRNA from the A site to the P site
EF-G
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Three stop codons
UAG, UAA, UGA
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What does release factor 1 do?
responsds to UAA and UAG
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What does release factor 2 do
respond to UAA and UGA
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What does release factor 3 do?
Relase RF1 and RF2 from the ribosome
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What happens when the RF's cleave the last aa-trna bond?
Release of the trna, mrna, protein, dissociation of the ribosome, rna recycling.
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What enzyme removes the formyl group fromthe N terminals of peptides
peptide deformylase
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What enzyme removes the N terminal methionine?
Methionine aminopeptidase
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What is the most important family of chaperone folding protiens
Hsp70 family
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Helper protiens that assist in the correct positioning of proteins
Sec system protiens
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Other cards in this set

Card 2

Front

How does it become and open complex?

Back

The B' pincer closes around the DNA and forms a channel and an active site. DNA strands separate without needed additional helicases

Card 3

Front

Where is the double helix opened, relative to transcription start?

Back

Preview of the front of card 3

Card 4

Front

What is often called the transcription bubble?

Back

Preview of the front of card 4

Card 5

Front

What needs to happen before the exposed bases are copied onto an RNA compliment?

Back

Preview of the front of card 5
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