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52 Cards in this Set
- Front
- Back
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If the second position of the codon is a purine, the AA will be _______ (what exception)
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Hydrophillic - except glycine.
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If the second position of the codon is a pyrimidine, the Amino acid will be _____
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Hydrophobic
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XYA and XYG are always the same amino acid, except
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Methionine/isoleucine and Stop/tryptophan
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XYC and XYU are always the same amino acid, except
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no exceptions, they are always the same amino acid
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what is the Wobble
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the third codon isn't super important, often A/G can be switched with U and the resulting Amino acid will be the same
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What is codon bias
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Some organisms have less tRNAs that are complementary for certain codon sequences, and so they have a bias towards certain codons to code for specific AAs
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How many arms are in a tRNA molecule, what are they called?
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5 arms:
Acceptor/Amino acid Arm Anticodon Arm extra arm D arm T(psi)C arm |
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Which arm is at the 3' end of tRNA?
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Acceptor/amino acid arm
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Where does aminoacyl tRNA sythetase interact with the tRNA molecule?
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the inner face of the tRNA, above the anticodon arm
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What do aminoacyl tRNA synthetases do?
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they esterify the amino acid to the tRNA molecule
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how many aminoacyl tRNA synthetases are there?
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one for each codon
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How many classes of aminoacyl tRNA syntheses are there?
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2
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What is the first step in the creation of an activated tRNA?
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the reaction of ATP + AA --> Aminoacyl-AMP + PPi
the formation of an acid anhydride -the same reaction occurs in both classes of tRNA |
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What part of the amino acid is the AMP molecule bound to?
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the Carbonyl carbon
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What is the second step in the creation of an activated tRNA molecule?
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Aminoacyl-AMP + HO-tRNA . The hydroxyl group on the 3' NT (adenine) attacks the Amino acid, displacing the AMP molecule
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HOw many ATP equips does it cost to activate a tRNA
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2 atp equivs
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How do aminoacyl tRNA syntheses recognize their cognate tRNA molecule?
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there are multiple recognition sites (like the arms, the anticodon, etc) that is unique to that tRNA that has the anticodon for a specific AA
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what makes up Ribosomes? (molecules?
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Ribosomal RNA (rRNA) and protein
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What are the 3 sites in the ribosome?
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A site (aminoacyl)
P site (peptidyl) E site (exit) |
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What is unique/special about the first methionine that gets incorporated into a polypeptide chain during protein synthesis
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It has a formyl group attached to it's Nitrogen.
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What do all prokaryotic proteins have that eukarytic proteins don't
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a formyl group attached to the first methionine (gets cleaved in euks, I think)
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How many tRNAs are there for met, how many Aminoacyl-tRNA synthetases for met?
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2 tRNAs. 1 aminoacyl tRNA synthetase
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What are the requirements for the initiation of Translation in proks:
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mRNA,
50s subunit, 30s subunit, tRNAfMet, IF-I, IF-II and IF-III, GTP |
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What happens if there is no shine dalgarno sequence in a prok mRNA 5' UTR?
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no translation
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Where does AUG interact with the ribosome (which site) during initiation
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P site
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Which site does IF-1 fill during initation
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the A site
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what is IF-3's role in initiation
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prevents the large (50s) subunit from binding to the small subunit
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Where is the complementary region to the shine dalgarno sequence?
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on the small ribosomal subunit
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What is IF-2's role in initiation
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it helps direct the fmettRNA towards the start codon (AUG), and if it matches, it catalyzes the hydrolysis of GTP--> GDP + Pi, and it kicks of the other 2 IFs
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Once all 3 initiation factors have been kicked off, and the large subunit associates with the fmettRNA, 30s subunit, and mRNA, what is this structure called?
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the initiation complex.
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Are the initiation factors part of the initiation complex
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no
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What are the requirements for the elongation stage of translation in proks?
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the 70s initiation complex
-mRNA -aatRNAs -GTP -EF-Ts, EF-Tu, EF-G |
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Which molecule catalyzes the addition of the next AA-tRNA molecule to the A site? What does this require?
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EF-Tu, When the Codon and anticodon match up in the A site, GTP is hydrolyzed to GDP by EF-Tu, and the next AA-tRNa is added.
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What catalyzes the formation of the peptide bond between adjacent AAs in the P and A site?
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the 23s RNA (ribozyme) within the Ribosome.
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Which elongation factor is responsible for translocation in the ribosome?
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EF-G
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What is translocation?
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Moving the tRNA from the A site to the P site, with the growing AA chain on the tRNA in the P stite. The tRNA in the P site moves to the E site.
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How many ATp equivalents are required to get 2 AAs in the P site? (with charged tRNAs)
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3 (1 for the first AA, 2 for the second)
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How many ATP equips does it take to get 10 AAs in the P site? (with charged tRNAs
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19 (1 for the first one, 2 each for the next 9)
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How many ATP equips does it take to get 10 AAs in the P site, without charged tRNAs?
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2x10 = 20 + 19 = 39
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How does Ef-G move the tRNA from the A site to the P site, and from the P site to the E site?
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It splits GTP-->GDP
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How does elongation stop?
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when the stop codon enters the A site, a release factor (RF-1 or RF-2) will bind at the A site.
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How does the bond between tRNA and the AA chain get broken? (after translation is complete)
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Hydrolysis, one water is used.
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What does tetracycline do?
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interferes with 16s rRNA, interacts with the shine dalgarno sequence and prevents translation
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What does streptomycin do?
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interferes with the 16s RNA, prevents translation
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What is the acronym for a Eukaryotic translational initiation factor?
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EIF
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What structures on EUK mRNA are vital for the formation of the translation initiation complex?
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the 5' guanosine cap, and the 3' poly A tail
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What is the analog to the shine dalgarno sequence in Euks?
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Trick questions- there isn't one- just need the 5' cap
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WHat is significant about the first codon in EUKS (compared to proks, 2 things)
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- It is does not have a formyl group (like proks)
-It is cleaved off after translation (unlike the prokaryote met group) |
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WHat is the proteasome?
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a barrell-like structure in the cell that contains several proteases for degrading proteins. It degrades proteins tagged with ubiquitin.
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Is the proteasome ATP dependent?
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Yes
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What enzyme adds ubiquitin to a protein that is needed for?
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Ubqiutin ligase - once a ubiquitin molcule is added, more ubuiqitin is added on.
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How many ubiquitin is added to a protein before it is sent to the proteasome to get degraded?
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4
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