Lecture 18 - Translation (pt 1)

Question 1

3 nuclear aspects of gene expression

Answer 1

Transcription, mRNA splicing, mRNA nuclear export

Question 2

3 cytoplasmic aspects of gene expression

Answer 2

mRNA stability, mRNA translation, protein stability

Question 3

How many ‘‘spare’’ codons we have

Answer 3

44

Question 4

To what extent are amino acids specific to a tRNA

Answer 4

Each amino acid has one OR more tRNAs

Question 5

How tRNA recognizes when an amino acid must be added next in a growing polypeptide

Answer 5

Recognizes a codon with its anticodon

Question 6

How rRNA is involved in translation

Answer 6

Makes up ribosome with proteins. One rRNA catalyzes peptide bond between N (amino group new a.a) and C (carboxy group growing chain)

Question 7

Direction of translation and which termini does the beginning of the growing polypeptide have

Answer 7

Translation 5’ to 3’ growing polypeptide has a N-termini at its beginning

Question 8

Name of the tRNAs bringing amino acids and what molecules are the ‘‘keepers’’ of the code/charge the tRNA with an amino acid

Answer 8

Aminoacyl-tRNA. Aminoacyl-tRNA synthetases.

Question 9

How aminoacyl-tRNA synthetase knows which tRNA to put with which amino acid

Answer 9

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

Question 10

Special name of the stem the aminoacyl-tRNA synthetase recognizes and how many aminoacyl-tRNA synthetases are necessary

Answer 10

Acceptor stem. There are aminoacyl-tRNA synthetases specific to each amino acid

Question 11

How proofreading of aminoacyl-tRNA synthetase works

Answer 11

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

Question 12

Name of the table with amino acids and corresponding codons

Answer 12

The genetic code

Question 13

What do we say about the genetic code if it’s doesn’t have a one to one correspondance

Answer 13

The code is degenerate

Question 14

What do we say about codons in the genetic code if some amino acids are encoded by different codons

Answer 14

There are synonymous codons in the code.

Question 15

What is reflected by the genetic code (and also the fact that it’s degenerate and that some codons are synonymous) (2)

Answer 15

1) Each tRNA anticodon is associated to an amino acid

2) Non-standard base pairs between anticodons and codons

Question 16

tRNA length, structure and 2 important regions

Answer 16

70-80 nt, clover-leaf structure. Acceptor stem and anticodon loop

Question 17

How many tRNAs in bacteria vs eukaryotic cells

Answer 17

30-40 vs 50-100

Question 18

What post-transcriptional modifications do tRNAs undergo

Answer 18

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

Question 19

Important base modification that happens to tRNA during processing and where these can occur (region of interest in the tRNA)

Answer 19

Deamination of adenine (by complexes) to yield inosine in bases in the anticodon loop. Can happen to bases of the anticodon

Question 20

Why anticodon:codon interactions are complex and what is VERY IMPORTANT about that

Answer 20

Anticodons can interact with more than one codon through non-standard ‘‘wobble’’ base-pairing OCCURING BETWEEN POS 1 ANTICODON AND POS 3 CODON

Question 21

Knowing that anticodons can interact with multiple codons, what is now variable in the genetic code ? (2)

Answer 21

1) Multiple tRNAs for one amino acid

2) Multiple tRNAs for one codon

Question 22

How positions of bases in codon/anticodon are numbered

Answer 22

On codon and on anticodon, it is 1,2,3 from 5’ to 3’

Question 23

What nts may be found in the anticodon and what nts may be found in the codon

Answer 23

Anticodon : CAGUI

Codon : CAGU

Question 24

Trick for the codon nts bound by each anticodon nucleotide (with the table)

Answer 24

Table : CAGUI. Below 1) Starting from C -> GUCAC 2) Starting from G-> UGA 3) Below I -> U

Question 25

In what sense are codons read ? so which position is the wobble

Answer 25

Codons (ex : GGA) are read 5’ to 3’ . Position 3 of codon is wobble so here it’s A

Question 26

Do we need a tRNA for each codon given wobble base-pairing on pos 1 anticodon

Answer 26

No, we can reach a minimum number of tRNAs for all codons of an amino acid

Question 27

Why do we say that there is punctuation in the genetic code

Answer 27

Start codon and stop codon

Question 28

Start codon and its amino acid

Answer 28

AUG -> methionine (Met)

Question 29

3 stop codons sequence

Answer 29

UAA, UAG, UGA

Question 30

2 characteristics of the way the codons are read

Answer 30

1) Code is comma-less : No empty space/unread codons between codons
2) Code is non-overlapping : 1 correct reading frame

Question 31

What do we mean by reading frame of an mRNA

Answer 31

By starting some nucleotides further (1 or 2), mRNA can be read in a totally different way

Question 32

What determines the number of possible reading frames of an mRNA

Answer 32

As many reading frames as there are nucleotides in a codon

Question 33

Why there is usually only one correct reading frame for an mRNA

Answer 33

Other reading frames blocked by numerous stop codons and are not translated

Question 34

Important thing to note independent of the reading frame concept

Answer 34

Codons are always read by jumping to the next 3 codons (never by shifting of 1 or 2 nts

Question 35

3 sites on the ribosome

Answer 35

A (for Amino acyl) site, P (for Peptidyl) site, E (for Exit) site

Question 36

What moves during translation and how perfect is the process of new aminoacyl-tRNA binding to the next codon

Answer 36

mRNA moves towards its 5’ end. Many amino acyl tRNAs try to bind on new codon until right one has good complementarity