Lecture 18 - Translation (pt 1) Flashcards
3 nuclear aspects of gene expression
Transcription, mRNA splicing, mRNA nuclear export
3 cytoplasmic aspects of gene expression
mRNA stability, mRNA translation, protein stability
How many ‘‘spare’’ codons we have
44
To what extent are amino acids specific to a tRNA
Each amino acid has one OR more tRNAs
How tRNA recognizes when an amino acid must be added next in a growing polypeptide
Recognizes a codon with its anticodon
How rRNA is involved in translation
Makes up ribosome with proteins. One rRNA catalyzes peptide bond between N (amino group new a.a) and C (carboxy group growing chain)
Direction of translation and which termini does the beginning of the growing polypeptide have
Translation 5’ to 3’ growing polypeptide has a N-termini at its beginning
Name of the tRNAs bringing amino acids and what molecules are the ‘‘keepers’’ of the code/charge the tRNA with an amino acid
Aminoacyl-tRNA. Aminoacyl-tRNA synthetases.
How aminoacyl-tRNA synthetase knows which tRNA to put with which amino acid
Binds constituants the bases in a groove of a stem structure in the aminoacyl-tRNA (and NOT its anticodon) and binds amino acid on other place
Special name of the stem the aminoacyl-tRNA synthetase recognizes and how many aminoacyl-tRNA synthetases are necessary
Acceptor stem. There are aminoacyl-tRNA synthetases specific to each amino acid
How proofreading of aminoacyl-tRNA synthetase works
Checks if a.a fits right in its pocket. If it doesn’t, it hydrolyzes its bond (that it just did) with the aminoacyl-tRNA and tries again
Name of the table with amino acids and corresponding codons
The genetic code
What do we say about the genetic code if it’s doesn’t have a one to one correspondance
The code is degenerate
What do we say about codons in the genetic code if some amino acids are encoded by different codons
There are synonymous codons in the code.
What is reflected by the genetic code (and also the fact that it’s degenerate and that some codons are synonymous) (2)
1) Each tRNA anticodon is associated to an amino acid
2) Non-standard base pairs between anticodons and codons
tRNA length, structure and 2 important regions
70-80 nt, clover-leaf structure. Acceptor stem and anticodon loop
How many tRNAs in bacteria vs eukaryotic cells
30-40 vs 50-100
What post-transcriptional modifications do tRNAs undergo
1) 5’ end cleavage and 3’ end cleavage
2) Addition of CCA at 3’ end (site of a.a binding)
3) Base modifications in the stem loops
Important base modification that happens to tRNA during processing and where these can occur (region of interest in the tRNA)
Deamination of adenine (by complexes) to yield inosine in bases in the anticodon loop. Can happen to bases of the anticodon
Why anticodon:codon interactions are complex and what is VERY IMPORTANT about that
Anticodons can interact with more than one codon through non-standard ‘‘wobble’’ base-pairing OCCURING BETWEEN POS 1 ANTICODON AND POS 3 CODON
Knowing that anticodons can interact with multiple codons, what is now variable in the genetic code ? (2)
1) Multiple tRNAs for one amino acid
2) Multiple tRNAs for one codon
How positions of bases in codon/anticodon are numbered
On codon and on anticodon, it is 1,2,3 from 5’ to 3’
What nts may be found in the anticodon and what nts may be found in the codon
Anticodon : CAGUI
Codon : CAGU
Trick for the codon nts bound by each anticodon nucleotide (with the table)
Table : CAGUI. Below 1) Starting from C -> GUCAC 2) Starting from G-> UGA 3) Below I -> U
In what sense are codons read ? so which position is the wobble
Codons (ex : GGA) are read 5’ to 3’ . Position 3 of codon is wobble so here it’s A
Do we need a tRNA for each codon given wobble base-pairing on pos 1 anticodon
No, we can reach a minimum number of tRNAs for all codons of an amino acid
Why do we say that there is punctuation in the genetic code
Start codon and stop codon
Start codon and its amino acid
AUG -> methionine (Met)
3 stop codons sequence
UAA, UAG, UGA
2 characteristics of the way the codons are read
1) Code is comma-less : No empty space/unread codons between codons
2) Code is non-overlapping : 1 correct reading frame
What do we mean by reading frame of an mRNA
By starting some nucleotides further (1 or 2), mRNA can be read in a totally different way
What determines the number of possible reading frames of an mRNA
As many reading frames as there are nucleotides in a codon
Why there is usually only one correct reading frame for an mRNA
Other reading frames blocked by numerous stop codons and are not translated
Important thing to note independent of the reading frame concept
Codons are always read by jumping to the next 3 codons (never by shifting of 1 or 2 nts
3 sites on the ribosome
A (for Amino acyl) site, P (for Peptidyl) site, E (for Exit) site
What moves during translation and how perfect is the process of new aminoacyl-tRNA binding to the next codon
mRNA moves towards its 5’ end. Many amino acyl tRNAs try to bind on new codon until right one has good complementarity
