Final-Ch.30

What proteins mediate eukaryotic translation elongation? What are they equivalent to in bacteria?

eEF1& eEF2 -> mediate elongation steps; eEF1 consists of two components: eEF-1A and eEF-1B. eEF-1A is the eukaryotic counterpart of EF-Tu; it serves as the aminoacyl-tRNA binding factor and requires GTP. eEF-1B is the eukaryotic equivalent of prokaryotic EF-Ts.

Describe how the chain termination phase works.

it requires G-protein. The elongation goes until it encounters a stop codon. The release factor protein sees "stop" and cause release of protein from ribosome. The RFP binds to the A site and recognizes the stop codon. All of them are G exchange proteins (GEF) G exchange factors. THey cause hydrolysis of the protein attached to tRNA.

What is in the nucleolus of eukaryotic cells?

rRNA genes are present in a tandem cluster of several hundred genes, which makes the nucleolus. Where rRNA transcription occurs. FGF usually promotes cell growth, is involved in rRNA transcription. This is translocated to nucleus and nucleolus after cell surface receptor binding.

Which parts of the tRNA are involved in aa tRNA synthetase recognition its correct one?

1. At least one base in the anticodon; 2. 1 or more of the 3 base pairs in the acceptor stem; and 3. the base at canonical position 73, referred to as the discriminator base because this base is invariant in the tRNAs for a particular amino acid.

Which component helps position the 30S subunit in alignment with the AUG start codon in the initiation phase of translation ?

16s RNA helps position 30S subunit in alignment with AUG start codon. It binds in the purine rich mRNA sequence, the ribosome-binding site, often called the Shine Delgarno (SD) sequence. The 3' ends of 16S rRNA binds to SD sequence.

Write the reaction that "charges" the tRNA with the correct amino acid. What enzyme catalyzes this reaction?

Aminoacyl tRNA synthetase

Describe the eukaryotic mRNA for translation and the function of any modifications

Eukaryotic mRNAs are characterized by two post-transcriptional modifications: the 5'-terminal methyl-GTP cap and the 3'-terminal poly(A) tail. The methyl-GTP cap is essential for mRNA binding by eukaryotic ribosomes and also enhances the stability of these mRNAs by preventing their degradation by 5'-exonucleases. The poly(A) tail enhances both the stability and translational efficiency of eukaryotic mRNAs. The Shine-Dalgarno (SD) sequences found at the 5'-end of prokaryotic mRNAs are absent in eukaryotic mRNAs.

In the elongation phase of translation, what part of the ribosome has the peptidyl transferase activity? Hydrolysis of which molecule drives translation.

GTP hydrolysis drives conformational changes that drive ribosomal functions. The acceptor ends (the aminoacylated ends) of both A- and P-site tRNAs interact with the peptidyl transferase center of the 50S subunit. Because the growing peptidyl chain doesn't move during peptidyl transfer, the acceptor end of the A-site aminoacyl-tRNA must move into the P site as its aminoacyl function picks up the peptidyl chain. At the same time, the acceptor end of the deacylated P-site tRNA is shunted into the E site. Then, the mRNA and the anticodon ends of tRNAs move together with respect to the 30S subunit so that the mRNA is passively dragged one codon further than the ribosome.

Describe how the Wobble hypothesis works.

It is the certain amount of play that might be allowed in base pairing at this position. The third base of the codon is sometimes referred to as the wobble position. The wobble rules indicate that a first-base anticodon U could recognize either an A or G in the codon third-base position; first-base anticodon G might recognize either U or C in the third-base position of the codon; and first-base anticodon might interact with U,C, or A in the codon third position. Some codons are used more than others. Abundant protein use preferred codons. Rare proteins use less used codons.

Describe how antibiotics block bacterial but not eukaryotic translation

Many bind key rRNA components- 2 main sites: 16S RNA decoding center and PTC of 23sRNA in large subunit. Why rRNA target? Difficult to defend against agents that bind rRNA. Many rRNA genes mutate 1-> Antibiotic resistance would only affect few rRNA's of total. RNA-4 basses vs 20 aa in protein would decrease the possibility for modification of rRNA so it retains function but losing antibiotic resistance. More likely to lose 1 then to lose both functions which is a lethal mutation

Describe how translation can be controlled.

Regulation of gene expression can be exerted post-transcriptionally through control of mRNA translation. Phosphorylation/dephosphorylation of translational components is a dominant mechanism for control of protein synthesis. Modification of some factors affects the rate of mRNA trnaslation. Peptide chain intiation, the initial phase of the synthetic process, is the optimal place for such control. c

What are the binding sites of aminoglycoside antibiotics? Macrolide antibiotics?

The decoding site is target of aminoglycoside antibiotics. Many antibiotics target PTC and peptide exit tunnel of macrolide antibiotics.

Describe how codon-anticodon pairing works.

The first two bases of the codon and the last two bases of the anticodon form canonical A:U or G:C base pairs in an antiparallel orientation, but pairing between the third base of the codon and the first base of the anticodon follows less stringent rules.

Describe the basis of the genetic code and all of its features.

The genetic code is a triplet code read continuously from a fixed starting point in each mRNA. It is defined by the following: 1. A group of 3 bases codes for 1 amino acid. 2. The code is not overlapping. 3. The base sequence is read from a fixed starting point without punctuation. If the reading frame is displaced by one base, it remains shifted throughout the subsequent message. 4. the code is degenerate, meaning that, in most cases, each amino acid can be coded by any of several triplets. A triplet code yields 64 codons for 20 amino acids. Noteworthy features characterize the genetic code: 1. All codons have meaning. 61 out of 64 specify a particular amino acids, while the remaining 3 specify no amino acid, thus are nonsense codons. 2. The genetic code is unambiguous. Each of the 61 "sense" codons encodes only one amino acid. 3. The genetic code is degenerate. With the exception of Met and Trp, every amino acid is coded by more than one codon. Codons coding for the same amino acid are called synonymous codons. 4. Codons representing the same acid or chemically similar amino acids tend to be similar in sequence Of ten the 3rd base in a codon is irrelevant, for example, all 4 codons in the GGX family specify Gly. 5. The genetic code is "universal". The codon assignments are virtually the same throughout all organisms-archaea, eubacteria, and eukaryotes. This conformity means that all extant organisms use the same genetic code.