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82 Cards in this Set
- Front
- Back
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Site of protein synthesis
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cytosol
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Template for protein synthesis
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mRNA
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Direction of translation
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5' to 3'
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Nonoverlapping code
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Sequence is read every three nucleotides, and each nucleotide is used only once.
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Unpunctuated code
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There are no "free" nucleotides between nucleotide triplets.
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Why nonoverlapping code?
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If a nucletide were used more than once, and it changed, it would affect multiple things; if it is used only once, and it changes, it affects only one thing.
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Why unpunctuated code?
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No need for punctuation; triplets are used as flags (like start, stop, etc)
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How many amino acids can a particular codon specify?
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one
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How many codes are there for amino acids?
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61; the other three specify STOP
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Degenerate code
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amino acids are specified by more than one codon
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Unambiguous code
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Each codon specifies only one amino acid.
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Why is the code degenerate?
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If there were 20 amino acid codons and 44 STOP codons, you would have a high probability of accidentally getting a STOP codon in any mutation.
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Changes in the first position of a codon tend to specify ...
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similar (or the same) amino acids
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Codons with pyrimidines in the second position tend to be ...
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hydrophobic
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Codons with purines in the second position tend to be ...
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polar
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A polar amino acid is most likely specified by a codon with a ... in the second position.
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purine
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A hydrophobic amino acid is most likely specified by a codon with a ... in the second position.
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pyrimidine
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When do xyU and xyC specify the same amino acid?
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Always
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When do xyA and xyG specify the same amino acid?
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Almost always - there are two exceptions.
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What are the three STOP codons?
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UAA
UAG UGA |
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Is every codon decoded by a unique tRNA?
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No - base pairing between the 3' end of the codon and 5' end of the tRNA "wobbles".
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What position does the wobble base occupy on the codon/anticodon?
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third position
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On what end of a tRNA anticodon would you find the wobble base?
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5' end of anticodon
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On what end of an mRNA codon would you find the wobble base?
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3' end of codon
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Where is inosine frequently found?
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5' end of the anticodon; the "wobble" base
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Inosine contains the deaminated adenine, known as ...
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hypoxanthine
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Inosine forms base pairs with ...
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uracil
cytosine adenine |
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Why is inosine frequently found in the wobble position?
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It base pairs with uracil, cytosine, and adenine
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What determines how many codons a tRNA can recognize?
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the wobble base (5' residue)
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Which bases in the wobble position allow for one codon to be recognized?
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C and A
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Which bases in the wobble position allow for two codons to be recognized?
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U and G
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Which bases in the wobble position allow for three codons to be recognized?
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I (inosine)
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In a wobble base, inosine can pair with ...
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A, U, or C
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In a wobble base, U pairs with ...
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A or G
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In a wobble base, G pairs with ...
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C or U
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Silent mutation
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Codon changes to a synonym; amino acid remains the same.
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Missense mutation (conservative)
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Codon encodes for a similar amino acid.
(eg, leucine to isoleucine) |
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Missense mutation (nonconservative)
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Codon encodes for a dissimilar amino acid.
(eg, leucine to arginine) |
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Nonsense mutation
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premature stop; changes the codon to specify STOP
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Read-Through mutation
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changes codon from STOP to an amino acid
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Frameshift mutation
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Nucleotide is inserted or deleted, shifting the triplet "frames" to the left or right.
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How many synthetases are there?
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20 - one for each amino acid
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What is an aminoacyl-tRNA synthetase?
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An enzyme that joins an amino acid to its specific tRNA
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What kind of enzyme joins the amino acid to its specific tRNA?
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aminoacyl-tRNA synthetase (aa-tRNA synthetase)
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Why does the amino acid need tRNA?
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Amino acid has O-, a poor leaving group; the tRNA on the other hand is a great leaving group.
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The "charging reaction" has two steps; name them.
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1. Amino acid is activated
2. Activated AA is transferred to tRNA. |
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By what mechanism is the amino acid activated in the charging reaction?
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Via formation of an aminoacyl intermediate on the enzyme.
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What bond joins the amino acid and the tRNA in aa-tRNA?
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ester linkage (O-C(-)=O
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aa-tRNA synthetase
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Joins aminoacyl group to tRNA
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What enzyme proofreads while joining aminoacyl-AMP to tRNA?
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aa-tRNA synthetase
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When aa-tRNA synthetase notices an incorrect aminoacyl-AMP, how does it correct the error?
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It hydrolyzes incorrectly activated tRNAs.
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How do synthetases discriminate between similar amino acids?
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Each synthetase is specific to an amino acid; eg, isoleucine is identified by isoleucyl-tRNA synthetase
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In aa-tRNA synthetase, where are the activation and proofreading sites in relation to each other?
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Separated.
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Synthetase needs to recognize two things for each joining:
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the tRNA and the amino acid
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What are the three steps within Initiation (of translation)?
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1. mRNA binds the ribosome
2. Reading frame is set 3. met-tRNAmet associates with AUG START codon |
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The AUG codon is bound to the ... of the ribosome.
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P site (peptidyl site)
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Which portion of the ribosome houses the P and A sites?
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small ribosomal subunit
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What is the role of IF1?
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Prevents tRNA from binding to the A site.
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What is the role of IF3?
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Prevents association of the large subunit (not ready for it yet)
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What purpose does the Shine-Dalgarno sequence serve in prokaryotes?
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It acts as a groove to align the ribosomal subunit with the START codon on the mRNA.
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The P site is home to ...
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the START codon (AUG)
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What role does IF2 play in initiation?
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It flags the Met-tRNA(fMet) to bind to the P-site on the ribosome.
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What happens after the initiation tRNA is bound?
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Initiation factors dissociate, the large ribosomal subunit joins and the initiation phase is complete.
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What is the initiation flag for prokaryotes? Eukaryotes?
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Prokaryotes: Met-tRNA(fMet)
Eukaryotes: Met-tRNA(Met) (notice no "f") |
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CBP complex
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cap binding protein; binds mRNA to the small ribosomal subunit
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What are the three substages of elongation?
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1. Aminoacyl-tRNA binding
2. Peptide bond formation 3. Translocation |
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What role does EF-Tu/GTP play in elongation?
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The incoming aa-tRNA is bound to it, and it binds to the A site of the ribosome.
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Name for tRNA in the A-site when it has both amino acids attached
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dipeptidyl-tRNA
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Dipeptidyl-tRNA leaves the tRNA in the P-site ...
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deacylated (uncharged)
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The ribosome slides down the mRNA by one codon
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translocation
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translocation
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Ribosome slides down the codon chain; dipeptidyl tRNA is now in P-site, the unacylated tRNA is in E site, and the A site is now open for the next amino acid.
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eEF
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eukaryotic elongation factor
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EF
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elongation factor
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EF-Tu (prokaryotic); eukaryotic counterpart?
(binds aa-tRNA and delivers to the A site) |
eEF-1(alpha)
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EF-TS (prokaryotic); eukaryotic counterpart?
(GEF or GTP/GDP exchange protein) |
eEF-1(beta-gamma)
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EF-G (prokaryotic); eukaryotic counterpart?
(translocase) |
eEF2
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Explain how EF-Tu works in terms of GTP, GDP, and affinity.
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EF-Tu/GTP has a high affinity for the A site; EF-Tu/GDP has a low affinity for the A site. EF-Tu/GTP binds the tRNA, brings it to the A site, becomes GDP, and releases itself.
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How is proofreading accomplished on the ribosome?
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No peptide bond is formed until EF-Tu is released; EF-Tu won't release until GTP is hydrolyzed to GDP.
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What regenerates EF-Tu/GTP after it is hydrolyzed to EF-Tu/GDP?
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EF-Ts; it is a GEF (Guanine Nucleotide Exchange Factor)
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GEF
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Guanine Nucleotide Exchange Factor
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eEF-1alpha is the eukaryotic version of EF-Tu; EF-Ts is the the GEF for EF-Tu. What is the GEF for eEF-1alpha?
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EF1betagamma
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What happens when the STOP codon enters the A-site?
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Release factors bind and hydrolyze the polypeptide, releasing it from the ribosome.
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