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1

What is the genetic code?

A set of 64 codons (triplet of nucleotides) that each code for one amino acid (some amino acids have multiple codons)

2

What does it mean to say that the genetic code is degenerate?

Most amino acids are represented by more than one codon

3

Degenerate codons tend to contain the same nucleotides in the ___ positions and vary in the ___ positions.

First and second; third (Wobble)

4

What is translation?

The process of translating mRNA into protein

5

True or false - the genetic code varies for different organisms.

False - the genetic code is universal in all organisms.

6

An mRNA consisting of contiguous triplet codons can be read in three different ___. How many are correct?

Frames; only one.

7

What are the 4 basic steps of translation?

1. Charging of the tRNA 2. Initiation 3. Elongation 4. Termination

8

Each ___ is specific for an amino acid.

tRNA

9

What synthesizes tRNA?

RNA Polymerase III

10

What is the anticodon?

A sequence of three nucleotides in the tRNA that base pairs with a codon in mRNA

11

tRNA is modified after synthesis; why?

Helps maintain its folding

12

Once the first two positions are paired, the exact pairing of the third position is less critical. This is the ___ position. What is the purpose of this?

Wobble; permits some tRNAs to recognize more than 1 codon.

13

For each wobble base codon, what are the possible anticodon bases? (U, C, A, G)

U -> A, G, I C -> G, I A -> U G -> C

14

If referring to the anticodon, the Wobble position is the ___ base. If referring to the codon, the Wobble position is the ___ base.

First; third.

15

What catalyzes the two-step activation of a t-RNA?

Aminoacyl-tRNA synthetase

16

Draw the two-step activation of a t-RNA.

17

The genetic code is translated by means of two adaptors that act one after another. What are these and what do they do?

1. Aminoacyl-tRNA synthetase - couples the amino acid to the corresponding tRNA

2. tRNA - its anticodon base pairs with a codon on the mRNA

18

How does the aminoacyl tRNA synthetase recognize the correct tRNA?

Extensive structural and chemical complimentarity; three adjacent binding pockets in the synthetase match the shape and charge of the nucleotides in the anticodon. 

19

How does the aminoactyl tRNA synthetase select the correct amino acid?

Proofreading activity via hydrolytic editing - an incorrect amino acid fits into the editing site and is cleaved. A correct amino acid does not fit, confirming that it is correct. The correct aminio acid has the highest affinity for the synthesis site (versus the editing site). 

20

The proofreading activity of aminoacyl-tRNA synthetase is very accurate; there is one mistake in ___ couplings.

40,000

21

Describe the process by which prokaryotes select the correct reading frame for protein synthesis.

Shine-Dalgarno sequences are located ~10 nucleotides upstream of the initiator codon in mRNA. These sequences are complementary to the 3' end of the 16S-ribosomal RNA in the prokaryotic 30S subunit. The ribosome is positioned for translation initiation in the correct reading frame by base pairing between the 16S rRNA and Shine-Dalgarno sequences. 

22

What are Shine-Dalgarno sequences?

Purine-rich sequences of 3-9 bases that bind the ribosome in prokaryotes in order to set the correct reading frame for translation.

23

How do eukaryotes select the correct reading frame?

eIF2 sets the frame; AUG start codon

24

What are the steps to initiation of protein synthesis in prokaryotes? 

1. The 30S subunit base pairs with the SD sequence upstream of the AUG start codon. This positions the initiating codon in the P site of the ribosome. 30S binds IF-3, preventing premature assembly with 50S.

2. A ternary complex between IF-2, GTP, and fMet-initiator tRNA binds in the P site of 30S, permitting base-pairing between mRNA initiation codon and fMet-tRNA (methionine-formyl methionine) anticodon.

3. The large complex formed in step 2 binds 50S subunit. GTP hydrolysis occurs and GDP, inorganic phosphate, IF-2, and IF-3 dissociate.

25

What do the subunits of the ribosome do?

The small ribosomal subunit accurately matches the codon and anti-codon. The large ribosomal subunit catalyzes peptide bond formation. 

26

What are the steps to initiation of protein synthesis in eukaryotes?

1. Initiator tRNA (with bound eIF2-GTP) is loaded into the small ribosomal subunit at the P site.

2. eIF4E and eIF4G bind to the 5' cap and the polyA tail of the mRNA, ensuring the mRNA is not broken. This aids recruitment of the 40S subunit (which has eIF2-GTP*met-tRNA), which binds to the mRNA at the 5' end.

3. eIF-4A and 4B facilitate the unwinding of the mRNA secondary structure so 40S can scan the untranslated region until a suitable AUG is reached. ATP hydrolysis catalyzes this step. 

4. eIF2-GTP is hydrolyzed, eIFs dissociate, and the large 60S ribosomal subunit binds to the 40S. Synthesis is ready to begin. 

27

What is the rate limiting step of translation initiation in eukaryotes and why?

The cleavage of eIF2-GTP to GDP; eIF2-GDP must be recycled to eIF2-GTP (catalyzed by eIF2B)

28

What are the steps to elongation in protein synthesis in eukaryotes?

1. Ribosomes contain 4 binding sites - mRNA site, A-site, P-site, and E-site. At the end of initiation, the initiation tRNA is in the P-site. An aminoacyl-tRNA molecule binds to a vacant A-site. 

2. A new peptide bond is formed between the amino acids in A and P. 

3. Large subunit translocates relative to the small subunit, leaving the 2 tRNA in hybrid sites (large in P, small in A, and large in E, small in P). This is catalyzed in part by the peptidyl transferase activity of the large subunit.

4. Small subunit translocates, carrying the mRNA 3 nucleotides and resetting the ribosome

29

In what direction does translation occur?

5' to 3'; N-term end of the protein is created first

30

Elongation requires what two things?

GTP hydrolysis and the participation of 3 elongation factors, including 2 GTP-binding proteins