Ch. 22: Protein Synthesis, Post Translational Modification, and Transport

Question 1

Codon

Answer 1

A triplet of 3 nucleotides which together form a genetic code for DNA or RNA

Question 2

tRNA (Transfer RNA)

Answer 2

The adaptor molecule, has the capacity to incorporate different kinds of bases

Question 3

What kind of complementary pairing does tRNA use?

Answer 3

Codon-anticodon base pairing

Question 4

Aminoacyl transferase

Answer 4

Enzyme required to catalyze the attachment of an amino acid to tRNA

Question 5

What does amino transferase do?

Answer 5

Attaches a specific amino acid to the 3’ acceptor stem of the cognate tRNA molecule

Question 6

AUG (Met)

Answer 6

The start codon

Question 7

What direction is the code read in with mRNA?

Answer 7

5’ to 3’ direction

Question 8

What does the D arm of tRNA do?

Answer 8

Makes sure that amino-acylation occurs

Question 9

Ribothymidine pseudouridine cytosine (T sai C loop)

Answer 9

Locates ribosomal binding site

Question 10

Acceptor Arm

Answer 10

Recognizes the cognate amino acid and binds to tRNA

Question 11

Inosine Base Pairing

Answer 11

Inosine in tRNA is formed by deamination of adenosine by the enzyme tRNA-specific adenosine deaminase

Question 12

What direction is tRNA in?

Answer 12

3’ to 5’ direction (Note: mRNA is antiparallel)

Question 13

Wobble Hypothesis

Answer 13

Base-pairing rules may be relaxed at the 3rd position of the codon (1st position of anticodon)

Question 14

Proofreading Functions of tRNA Synthetases (Correct)

Answer 14

When the correct tRNA (tRNAThr) and cognate amino acid (Thr) bind to the active site in step 1, then amino acylation occurs in the active site and this amino-acylated tRNA is not hydrolyzed by the editing site in step 2, thus generation the correct aminoacylated tRNA (the-tRNAThr)

Question 15

Proofreading Functions of tRNA Synthetases (Incorrect)

Answer 15

When a chemically similar, but incorrect, amino acid (Val) binds loosely to the active site with the same tRNA (tRNAThr) in step 1, then the aminoacylated tRNA is still generated. However, the incorrect amino acid is hydrolyzed at the editing site in step 2

Question 16

AUG

Answer 16

Start codon for both prokaryotes and eukaryotes

Question 17

Translation

Answer 17

Protein synthesis, occurs on the ribosome

Question 18

Where is translation terminated?

Answer 18

Terminated by stop codons on the mRNA transcript; release factor binds to the ribosome in place of a charged tRNA, and the polypeptide chain is released from the ribosome

Question 19

Ribosomal Complex

Answer 19

Recruitment of a large subunit to a small subunit

Question 20

Where does the ribosomal complex land?

Answer 20

On one of three sites:
1. E site (Exit site)
2. P site (Peptidyl site)
3. A site (amino acyl site)

Question 21

Initiation (Prokaryotic)

Answer 21

Uses 30S and 50S subunits to form the 70S ribosome
Three initiation factors involved
Shine-Dalgarno sequence appears 5-13 base pairs upstream of the first AUG codon to orient mRNA within the ribosome

Question 22

Initiation (Eukaryotic)

Answer 22

Uses 40S and 60S subunits to form the 80S ribosome
Requires specific mRNA sequences at both the 5’ and 3’ ends of the mRNA (5’ cap is a vital feature that protects mRNA during transport)
Multiple elongation factors as well as GTP and ATP

Question 23

Steps of Initiation (Prokaryotes)

Answer 23

1. Met recognizes correct tRNA and binds
   Gets methylated (FMet tRNA)
2. The mRNA and fMet-tRNAMet bind to the complex with the Shine-Dalgarno sequence of mRNA aligning with the complementary sequences in the 16S rRNA in the 30S ribosomal subunit, and IF3 is released
3. Hydrolysis of GTP facilitates binding of the 50S ribosomal subunit, with the release of IF1 and IF2 to form the functional 70S ribosomal initiation complex. Conists of fMet-tRNAMet bound in the P site, with the E and A site empty until elongation begins

Question 24

Steps of Initiation (Eukaryotes)

Answer 24

1. 43S pre-initiation complex is formed between the 40S small ribosomal subunit and a complex consisting of the elF2, elF3, elF5, elFA, the amino-acylated met-tRNAimet, and GTP
2. mRNA transcript (contains a number of RNA binding proteins associated with the 5’ cap and poly A tail) associates with the 43S pre-initiation complex to form the 48S pre-initiation complex
3. 60S large ribosomal subunit associates with the 48S pre-initiation complex, resulting in the exchange of initiation factor proteins and the formation of the fully assembled 80S complex

Question 25

Which of the following is similar in eukaryotes and prokaryotes: Initiation, elongation, termination

Answer 25

Elongation

Question 26

Elongation

Answer 26

The 6 step elongation cycle requires the hydrolysis of 2 GTP, one to promote the binding of the AA-tRNA^AA to the A site, and one to facilitate translocation of the ribosome in the 3' direction

Question 27

How many GTP does translational elongation require?

Answer 27

2 GTP

Question 28

What does each of the two GTP molecules do in elongation?

Answer 28

1. Promote the binding of the AA-tRNA^AA to the A site 2. Facilitate the translocation of the ribosome in the 3' direction

Question 29

Peptidyl transferase reaction

Answer 29

Creates a peptide bond that holds the polypeptide together

Question 30

How does the peptide transferase reaction work?

Answer 30

The amino group of the amino acid attached to the 3' terminus of the tRNA in the A site attacks the carbonyl carbon of the peptidly-tRNA in the P site, resulting in an extended A-site peptidyl tRNA

Question 31

Release of the polypeptide

Answer 31

Release factors bind to the termination codon and lead to the release of the polypeptide chain

Question 32

How many termination codons are there?

Answer 32

3 Stop Codons: UAG, UGA, UAA

Question 33

What bases can inosine wobble with?

Answer 33

A, C, U

Question 34

In the wobble phenomenon, the base that wobbles is found in the ___?

Answer 34

tRNA

Question 35

How many codons are known for each amino acid?

Answer 35

1 to 6 depending on the nature of the amino acid

Question 36

Are there any exceptions to the universality of the genetic code?

Answer 36

Yes, in mitochondria and 16 other organisms, including some algae and fungi

Question 37

Which amino acids have unique codons?

Answer 37

1. Trp 2. Met (AUG)

Question 38

The genetic code is said to be degenerate. What does this mean?

Answer 38

Many amino acids are coded for by different codons.