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52 Cards in this Set
- Front
- Back
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The large subunit of the bacterial ribosome has _____ and _____ proteins.
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2 rRNAs (5S and 23S); 34 proteins
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The small subunit of the bacterial ribosome has _____ and _____ proteins.
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1 rRNA (16S); 21 proteins
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How do mRNAs react with the ribosome?
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It lies between and contacts both parts.
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The overall prokaryotic ribosome is _____.
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70S
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Information stored in a nucleotide sequence is _________ by tRNAs.
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translated into information in a polypeptide (AA sequence)
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What are the functions of the: 1) anticodon loop; 2) 3' A ; 3) other loops
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1. it is complementary to the codons on the mRNA, so they attach.
2. The A attaches to the right amino acid. 3. They interact with ribosomal proteins. |
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What is the role of aminoacyl-tRNA synthetases?
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They charge tRNAs with the correct amino acids via ATP. (They attach the amino acid with the tRNA).
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How is the amino acid attached to the tRNA? (Hint: what type of bond, where are they attached...)
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They are attached by a high energy ester bond at the last A at the 3' end of the tRNA. This provides energy for the formation of a peptide bond by ribosome.
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How does the tRNA fix any mistakes?
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By proofreading. If there is a mistake, the bond is ydrolyzed.
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There are ___ potential codons.
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64
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How many stop codons are there?
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3
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What is a stop codon?
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one that has no complimentary anticodon, therefore it has to stop making it.
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The code is ______.
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degenerate - this means that there are up to 6 different codons that can encode for the same AA.
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What does the wobble effect do?
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it allows all 61 codons with fewer tRNAs and AA-tRNA synthetases.
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For initiation of translation in bacteria, ribosomes must....
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first be dissociated. When this happens, IF3 binds to 16S rRNA and keeps the 30 & 50 subunits apart.
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How is the mRNA correctly aligned?
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By the complementary binding of 16S rRNA to the Shine-Dalgarno sequence at 5' end. This positions the AUG site for the P site on the 50S unit.
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How does the first amino acid bind to the mRNA? Where does it bind?
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a tRNA with a formylmethionine attached binds to IF2 and GTP. These come together and bind at the P site.
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What occurs after the tRNA has bound to the P site?
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IF1 attaches and GTP gets hydrolyzed. This then expels all initiation factors and then 50S unit binds.
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How many cycles are in translation elongation?
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2 cycles.
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After initiation of the translation of elongation, what complex binds where?
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a complex of the next charged tRNA, GTP, and Elongation Factor-Tu (EF-Tu) binds to the A site.
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Why does tRNA bind to a complex before attaching to the RNA?
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Because the energy released by the complex helps to accurately put where the tRNA belongs on the RNA.
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Explain the movement of the AA's during the first cycle of elongation?
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There are AA's that are on the P-site originally. When a tRNA is placed in the A-site, the 23S rRNA ribozyme uses peptidyl transferase to move the AA's from the P site to the A site. No extra energy is required, as it occurs during GTP hydrolysis of the first cycle.
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Explain the first cycle of elongation in full.
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You have a GDP + EF-Tu. EF-Ts binds to it and releases the GDP. GTP then binds to EF-Tu + EF-Ts. This releases EF-Ts. The AA-tRNA then attaches to the EF-Tu + GTP. The AA-tRNA is then placed in the A-site while GTP is hydrolyzed.
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Explain the movement of the AA's during the second cycle of elongation (translocation)?
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The AA's don't relocate, instead the tRNA's move. The tRNA that was in the P-site, moves to the E-site. And the tRNA-AA that was in the A-site, moves to the P-site.
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Explain the second cycle of elongation in full.
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EF-G + GDP. GDP leaves and then GTP binds. This complex gets hydrolyzed and the tRNAs move. Start over again.
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What are the stop codons?
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UAA, UGA, or UAG.
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When does termination occur?
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When the ribosome translates a stop codon (meaning, no tRNA with an anti-codon exists).
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What are the exceptions to the stop codons?
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tRNA with selenocysteine is made with some UGA's in all domains. tRNA with pyrrolysine is made with some UAG's in prokaryotes.
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What factors are needed for translation termination?
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RF-1, RF-2, or RF-3 depending on the stop codon, and GTP hydrolysis.
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The protein sequence does not yield....
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properly folded proteins. This means their function may not be used until proper three-dimensional shape.
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_____ aid in the proper polypeptide folding.
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Chaperones
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What is the trigger factor?
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Proline isomerase.
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How are DnaJ and DnaK used?
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The mostly straighten out proteins and then rework them to put them in the right conformation. However, sometimes they are not enough and the GroEL/GroES system is needed. They require ATP.
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How is GroEL/GroES used?
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When DnaK and DnaJ aren't enough they use a barrel system to rework the proteins. ATP is required.
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In some proteins, what is removed and what can be done?
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the f-met and sometimes NH2 terminal AA's are removed. Some proteins self-splice.
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The Sec system is...
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a highly conserved secretion system found in all domains.
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In Sec-dependent protein export, polypeptides must contain...
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signal peptide at the NH2 (amino) terminal end that binds to Sec proteins in order to be exported.
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What is the purpose of Sec B?
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It keeps polypeptide unfolded.
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What is the purpose of Sec A?
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it interacts with the Sec YEG channel and drives the polypeptide through the channel using ATP.
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Once the polypeptide chain has made it through the channel, what happens?
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It gets refolded on the other side of the cell by chaperone proteins.
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What is the purpose of signal peptidase?
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It cleaves the signal peptide.
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Explain the Type 1 complex system.
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It is an ABC exporter that expands all layers; it exports proteins (lipases, toxins, antibiotics) outside the cell. All prokaryotes use this. ATP hyrdolysis drives this system.
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Explain Type II & V.
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They use the SEC proteins in the first step and then other proteins.
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Explain Type III complex system.
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Used by gram negative pathogensto directly inject proteins into a host cell during infection
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Explain Type VI complex system.
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Very similar to Type III. They inject DNA as well as proteins during conjugation.
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Explain the TAT system.
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TAT means Twin Arginine System. It's when two arginines are moved across. It uses a PMF.
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What are the building blocks for the cell wall?
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NAM-pentapeptide and NAG.
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Explain the synthesis of peptidoglycan for the cell wall.
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UDP-linked NAG or NAM is formed, the pentapeptide is assembled on NAM. NAM-peptide is then transferred to bactoprenol carrier (BP). NAG is then transferred to NAM, and then the whole unit is transferred across the CM by BP.
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Linking of the growing NAG-NAM chain and transpeptidation occurs _____.
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outside of the cell.
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Cycloserine inhibits the formation of ____.
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D-alanine.
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What inhibits the transpeptidation step in peptidoglycan synthesis?
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Vancomycin and penicillin
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What does bacitracin do?
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It inhibits bactoprenol from transporting back into the cytoplasm to keep the cycle going.
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