Module 04 - Section 04

Question 1

What is the 2D shape of tRNA and its 3D shape

Answer 1

2D: clover leaf with 4 arms
3D: L-shape

Question 2

Describe the amino acid arm of tRNA

Answer 2

Contains a trinucleotide sequence CCA at the 3’ terminus - the 3’-terminal A residue if the nucleotide to which the amino acids attach – each tRNA carry a specific amino acid making aminoacylated

Question 3

Describe the anticodon arm of tRNA

Answer 3

three-nucleotide sequence that base pairs with the mRNA (complementary)

Question 4

What is tRNA called when bound to its amino acid?

Answer 4

aminoacyl-tRNA or said to be charged?

Question 5

What provides specificity to tRNA?

Answer 5

the enzymes that attach the amino acids to particular tRNAs - called aminoacyl-tRNA synthetases

Question 6

What is the denoting convention for

a) uncharged tRNA specific to leucine
b) charged tRNA specific to leucine

Answer 6

a) tRNA^Leu

b) Leucyl-tRNA^Leu or Leu-tRNA^Leu

Question 7

Which enzyme is responsible to make sure the correct amino acid is added?

Answer 7

aminoacyl-tRNA synthetases

Question 8

What is Wobble base pairing?

Answer 8

Noncanonical base pairing that can only happen in the third position of the mRNA codon (5’ nucleotide in anticodon)

Question 9

What is the wobble position?

Answer 9

nucleotide at the 3rd position of the codon which can vary without affecting the encoded amino acid

Question 10

What is Inosine?

Answer 10

Adenoside that has been converted to inosine through the actions of adenosine deaminase action on RNA

Question 11

Which nucleotides can Inosine form base pairs with?

Answer 11

A, C or U in the 3rd position of the mRNA codon

Question 12

What are the 4 relationships of the Wobble hypothesis?

Answer 12

(1) the first 2 bases of an mRNA codon always form watson-crick base pairs and confer most of the coding specificity
(2) 1st base of the anticodon determines the number of codons recognized by tRNA
- when A or C - only one codon recognized
- when U or G = 2 codons recognize
- when I = 3 different codons
(3) When an amino acid is specified by several codon, codons that differ by either of the first two bases required different RNAs
(4) A minimum of 32 tRNAs are required to translate all 61 codons (31 for amino acids and 1 for initiation)

Question 13

What is resposible of the functional activity of the ribosome?

Answer 13

rRNA

Question 14

describe the subunits of ribosome

Answer 14

Small unit of 40S and Large unit of 60S which combine to form the functional 80S ribosome

Question 15

Discuss the relation between amino acids, tRNAs and the ribosome

Answer 15

All 3 are intimately involved in the process of translation
Amino acids are the building blocks of proteins
tRNAs function as adaptor molecules to carry amino acids to the growing polypeptide
Ribosome are the protein factory within the cell

Question 16

What catalyzes the peptide bond between adjacent amino acid?

Answer 16

Peptidyl tranferase center, located in the 60S subunit

Question 17

What and where is the decoding center in ribosomes?

Answer 17

It is where aminoacylated tRNAs read the genetic code by base pairing with tripled codon in mRNA. It is located in the 40S subunit of the ribosome

Question 18

What is the A site?

Answer 18

location where the Aminoacyl-tRNA binds (charged tRNA)

Question 19

What is the P site?

Answer 19

Location of the Peptidyl-tRNA binding (tRNA that contains the growing polypeptide chain)

Question 20

What is the E site?

Answer 20

the Exit site, occupied by the tRNA molecule released after the growing polypeptide hain is transferred to the aminoacyl-tRNA in the PO site

Question 21

What is the sequence of “sites” a tRNA goes through in a ribosome?

Answer 21

A-P-E

Question 22

What are the 5 steps of translation?

Answer 22

(1) initiator tRNA is charged with methionine
(2) Translation initiates with the assembly of mRNA and aminoacylated tRNA on the small ribosomal subunit, followed by joining with the large subunit = ribosome active
(3) Polypeptide elongation occurs in successive cycles of aminoacyl-tRNA binding and peptide bond formation
(4) Translation stops when the ribosome encounters a stop codon in the mRNA, leading to release of mRNA and dissociation of ribosome into 2 subunits
(5) Polypeptide fold during or immediately after transaltion

Question 23

What are the 3 steps of initiation of translation?

Answer 23

(1) Alignment of mRNA on the small ribosomal subunit - IF-3 associates with the small unit to prevent premature assembly of ribosome
(2) Association of a charged initiator tRNA with the AUG start codon in the Psite
- this tRNA is shephered to the ribosome by IF-2 to ensure the correct alignment of the tRNA
(3) Recruitment of the large ribosomal subunit to form a complete initiation complex
- IFs dissociate from the complex which consumes GTP

Question 24

What is considered the energy currency of translation

Answer 24

GTP

Question 25

Which stage of translation is the most regulated?

Answer 25

Initiation

Question 26

What is the Shine-Dalgarno sequence and what is its use?

Answer 26

Consensus sequence of 4-9 purines residues situated 8-13 nucleotides on the 5' side of the start codon It is an Initiation Signal, which base pairs with a complementary pyrimidine rich sequence near the 3' end of the 16S rRNA ribosomal small subunit

Question 27

What are the 2 bacterial tRNA specific for methionine?

Answer 27

``` tRNA^fmet = initiation codon tRNA^met = within the mRNA transcript ```

Question 28

Why can't methionine be added to the transcript of mRNA (internally aka anywhere else than the 1st amino acid)?

Answer 28

A transformylase enzyme transfers a formyl group to the amino group of Methionine -- essentially, this blocks the N-terminus and thus it can only be the first amino acid because it can no longer be added at the C' end

Question 29

What is Polycistronic mRNA?

Answer 29

A contiguous mRNA with more than 2 gens that can be translated into proteins

Question 30

What is a monocistronic mRNA

Answer 30

Encoding a single proteins

Question 31

Match eukaryote and prokaryote to polycistronic and monocistronic

Answer 31

``` eukaryote = monocistronic prokaryote = polycistronic ```

Question 32

What are Kozak sequences?

Answer 32

A sequence around the start codon in eukaryotic mRNA taht guides translation. The Kozak sequence has a purine nucleotide three residues before, and a G residue immediately after, the start codon

Question 33

What are the functions of the interactions between the eukaryotic IF with the 5' cap or poly(a) binding protein which are associated with the 3' poly(A) tail of the mRNA?

Answer 33

(1) ensuring that mRNA processing is complete prior to translation (2) Promoting translational efficiency (3) enabling the sophisticated translation regulation of gene expression